Adapsin: 4 ESS-Karma and 12 Karma in
Y for a -10% to Cyberware ESS cost. Not available at Chargen, Adapsin, on it's face, should be a reasonable choice for anyone planning on taking more than 2.0 ESS in cyberware in the future, but where Adapsin really shines is for someone who wants to become a cyberlimb monster, the guys that want to go whole-hog and are getting all 4 limbs, torso and skull - normally these cost 6.25 ESS (so, not possible without Alphaware or a Quality), with Adapsin it's 5.625 ESS. Throw in Biocompatability (Cyberware) with this and you've got a full 1 ESS to work around - alpha, beta and deltawares would only make it even better. Isn't cyber-life grand?
Daredrenaline: 2 ESS-Karma and 10 Karma in
Y for to +1 WIL tests. This includes Stun Damage and Spell Resistance - as well as all WIL-linked Skill tests. So although you don't get the Stun Box, this is nearly as good as a full point to your WIL attribute. Accordingly, it really doesn't make sense unless you already have a 3 or higher WIL attribute. Then when you take into consideration you essentially acquire a (slightly worse version - threshold 3 - of a) 10 Karma (5 BP) Negative Quality (Poor Self Control - Thrill Seeker) with this genetech, it's benefits become more dubious. If you're an already Augmented Magician, you can get +1 Drain Resistance dice here, and that may be worth it, PCs who already have the Thrill Seeker Neg Quality also have less to lose from this.
Dynomitan: 4 ESS-Karma and 12 Karma in
Y for +1 to all INT skill tests. Skills highlighted here would mainly be Perception, Shadowing, Disguise, and Assensing for Awakened PCs (yeah, there are 5 others, but they're pretty niche). Considering that you also pick up what could be a 10 (if not 20) Karma Neg Quality with this Genetech, AND all the other ways to Augment Perception and even all INT Skills, this really isn't a very good piece of 'ware. In fact, you should probably never buy it for any build.
Neo-EPO: 4 ESS-Karma and 12 Karma in
Y for +1 to all Athletics and Fatigue tests. It's not much cheaper than Enhanced Articulation (and does less) and is considerably more expensive than Synthcardium (and does less), but it is a dice pool modifier so it will stack - so if Athletics are a big part of your thing, go ahead and pick up Neo-EPO too, just make sure it's the very last Athletics-augmentation you buy.
PuSHeD: 2 ESS-Karma and 6 Karma in
Y for +1 to all LOG skill tests(!). Considering LOG has the largest skill-pool beneath it, PuSHeD is a great deal for any LOG-skill-oriented PC, Hacker, Rigger, Medic, etc., preferable to Encephalon by a long shot. There really is nothing bad to say about this bit of Genetech.
Qualia: 8 ESS-Karma and 10 Karma in
Y for a +1 to all INT Skill tests. I don't know what they think is so great about INT Skills, not like this helps your intiative, but at least you don't acquire a Negative Quality for it. It is one of two ways to Augment INT skills, and it's the worse of the two. It is a dice-pool modifier though, so if you're trying to squeeze the most out of those INT skills, it's here.
Reakt: 8 ESS-Karma and 12 Karma in
Y for a +2 to REA based Defense Tests. So maybe it could be reckoned as like buying 1/3 of 2 points in REA (no skill or initiative benefits)? So, it's worth 8 Karma and up? That's not really accurate though. Passive Dodge is (IMHO) extremely important for Primary Combatants, avoiding damage completely is more efficient than soaking it, in any circumstance - the problem being you're putting an Attribute-Only Pool up against an Attribute+Skill Pool. Still, any Primary Combatant can benefit from this 'ware - though it's especially worth it as a cap-stone for those with an already elevated REA (say, through WR and REA Enhancers).
Synch: 6 ESS-Karma and 12 Karma in
Y for +1 to Perception and a very rare +1 to all Combat Skill Tests (including Defense). It's got this quirk where it doesn't kick in until the enemies first attack, so I think this is why it isn't more popular (I know our group went through our first two sessions without our enemies ever firing a shot), but otherwise this is a really good bit of 'ware, recommended for any Primary Combatant.
Limbic Nanoware: Including Nanohive, the Limbic Nans cost a minimum of 15 ESS-Karma and 6 Karma in
Y, up to 10 Karma in Y, for +1 - 3 to all INT Skill Tests. If you're augmenting your INT Skills go with this route, and you should go all in with the Rating 3 Limbic Nans - it doesn't cost you anymore ESS than Rating 1, just a few more Y. Really, though, if you're getting Limbics, you're getting a Nanohive so you should at least get a Rating 2 Hive so you can cram some more cheap augs into the ESS-expensive Hive. Like....
Neocortical Nanoware: same deal as the Limbics, costs a minimum of 15 ESS-Karma and 6 Karma in
Y, up to 10 Karma in Y, for +1 - 3 to all LOG Skill Tests. If you're a Hacker or otherwise LOG-Skill oriented character, you should seriously consider Neocorts. Better than Encephalon, better than PuSHeD (because you can get up to +3), this is just the way to go to boost your LOG skills you can't do without.
Cyberlimbs: Such a classic trope of cyberpunk, but such oh-so-complex rules! Why!?! What skills can I apply X limb to? What is my situational BOD vs. my overall BOD? Or STR? Or Armor?! Ohhh, the trans-humanity! ... ...
Cyberlimbs are fun, you can do some unique things with them, for that reason (among others...) they're hard to judge the Karma efficiency of. So what we're gonna do instead is look at some comparative purchases. Let's say the scenario is a 5 AGI Human, and compare an Obvious, Custom Full Arm (3 BOD, 3 STR, 9 AGI) to the purchase of Rating 4 Muscle Toner, looking to improve his primary pools (combat and stealth).
The cyberlimb costs 20 ESS-Karma and just short of 9 Karma in
Y, the Toner costs 16 ESS-Karma and 22 Karma in Y and Restricted Gear. The 'limb is more expensive in ESS, but considerably less expensive in chargen resources in general. Of course, the limb's AGI only applies to actions taken with that limb only - which pretty much equals single arm attacks (but could also conceivably include Forgery, Locksmith and Palming), and assuming the BOD and STR are equal to the PCs naturals, the rest is a wash (though you do gain +1 Phys Soak Box). So, what we end up with is 1/2 of the functionality (you lose Gymnastics, Infiltration and any two-handed weapon or full-body attack, so Archery, the big Automatics, Longarms, and Unarmed Combat, as well as other Skills) for about 3/4 of the total cost in resources. This would lead us to the reasonable conclusion that such Cyberlimbs are probably not a good deal for Stealthy Primary Combatants - who are generally ESS-intensive, but possibly not a bad option for characters who aren't concerned with stealth and their combat role is only supportive - and plan on using one-handed weapons (Blades, Clubs, Pistols, Sub-MGs, Throwing Weapons), who aren't necessarily otherwise ESS intensive (so maybe a Hacker or Face could have reasonable cause).
A STR cyberlimb would compare similarly, because although the main function of STR for a combatant is increasing melee damage, you would gain almost no benefit to the STR-linked Skills without all 4 limbs - which is very ESS intensive, quite like Muscle Replacement, which is why I recommended that if you are considering Muscle Replacement, just get cyberlimbs instead. You can ultimately get the same benefit for the same massive ESS-cost (albeit more
Y) but there's so many additional fun things you can put into cyberlimbs - like Gyromounts, Hidden Slides and Holsters, and Cyberweapons, etc. so how do we weigh those in? Really what the ultimate conclusion is, is that taking a Cyberlimb should largely be made on the level of flavor and RP choices - if it's a cyberpunk trope that you love and wish to honor, you can absolutely make effective use of it, it may not be optimal in all regards or circumstances - but the Rule of Cool ... well, it rules.
Part 4: the Others – Qualities, Spells, Contacts, Martial Arts, etc.
Qualities: First off, you should always take your full -35 BP (70 Karma) in Negative Qualities, not only are these great for crafting your PCs story and flavor, but you can also usually end up with a fairly mechanically innocuous set of Qualities, for a significant gain. With Posi-Qualities you can grab some Skill, Attribute and ability bonuses that are not available anywhere/way else. Where are the good deals and where are the lemons?
+1 or 2 to X-Skill or Test(s): there are lot's of Qualities (Animal Empathy, Codeslinger, Double Jointed, First Impression, Guts, Home Ground, Quick Healer, Analytical Mind, Catlike, Inspired, Linguist, Natural Athlete, Outdoorsman, Perceptive, School of Hard Knocks, Tech School Education, Trustworthy, Water Sprite, and maybe others) that give a bonus of +1 or 2 dice pool or skill modifier to one or more Skills or specific Tests. In general, these are not good investments unless you are trying to be a best of the best specialist in regards to the Skill(s) or Test to which the Quality pertains.
Some stand out (Codeslinger, First Impression, possibly Quick Healer - if you take some 'ware for synergy, and Home Ground for NPCs) as being better deals than the others. Some stand out (Home Ground for PCs, Perceptive and Trustworthy) as options that you should never take. All the rest again should probably only be taken if you're trying to be the best around at that particular thing.
Ambidextrous: don't dual-wield firearms unless you take this, and don't take this unless you're going to dual-wield (i.e. it's a specialist thing).
Aptitude: Spending 20 Karma for the ability to spend 14 Karma to get 1 more dice in any skill is a dubious option, at best. Aptitude is something that should only be taken by a PC who is trying to be the best of the best in X Skill, and even then only if the Skill is not easily Augmented (so Combat Skills are good options - LOG, INT, and Physical/Athletic Skills are bad options). If you're thinking about taking Aptitude, look through the above mentioned "+1 or 2 to X-Skill" Qualities first, as you may be able to get that die, or more die, cheaper.
Exceptional Attribute: 40 Karma to up a Natural Attribute Maximum by 1. There are two other ways to do this, one is a Metagenetic Quality and therefore will not be covered explicitly here and the other is Bioware/Genetech, covered above. Exceptional Attribute is the worst of these options. Exceptional Attribute is only appealing in 2 cases: the first is for a PC who is going "all in" on boosting a single Attribute. So, if you're taking Metagenetic Improvement AND Genetic Optimization both in a single Attribute, it's not a horrible idea to top it off with Exceptional Attribute - especially if it gets you that extra Augmented Maximum die. Also, it's more appealing if you're choosing an Attribute that isn't easily Augmented with 'ware (so AGI, STR, REA and LOG are bad options - that extra 1 die likely just isn't worth the investment). So, All-In Specialists or maybe an already Augmented Magician might benefit from boosting a Drain Attribute would reasonably choose this.
Focused Concentration: it's a tempting Quality, because dealing with Drain is perhaps a Magicians biggest concern so there could always be a compelling argument for this Quality - espcially if you're an Over-caster type. You're probably either dealing with Drain by choosing spells and force carefully or you're just doing everything you can to pump up those Drain Attributes - this Quality is the next best thing.
High Pain Tolerance: Strictly worse than Damage Compensators, each level of HPT costs 10 Karma, where each level of DCs costs 8 Karma (2 of that in ESS-Karma). Though it's not by much, so if you're tight on
Y and/or ESS, you could consider this Quality. Note though that you'll never be able to pick up any other forms of damage compensation with the Quality...
Lucky: oh, Lucky Quality - how unlucky is he who chooses you? 40 Karma for the potential of 1 more point in EDG. Even if your GM refreshes EDG every second, this Quality is not worth it. Seriously though, even if you're building a Mr. Lucky Character with an EDG-friendly refresh policy, this Quality (much like Exceptional Attribute) is usually a bum deal. Perhaps this advice is tinted by my own lack-luster experience with EDG, but I generally find it's better to invest your resources in just being consistently good at what you do.
Magic Resistance: I get healed by my own Magician a lot more than I am targeted by the Spell of another Magician. This is not a good Quality.
Murky Link: No. Just no.
Natural Hardening: You can buy a Rating 7(!) Biofeedback Filter for as much as this Quality costs... don't take this Quality.
Natural Immunity: extremely narrow applicability makes this a bad choice for any PC (or NPC) who is not using it to make himself immune to a buffing drug.
Photographic Memory: a fairly intangible yet decidedly niche mechanical benefit... probably not worth the cost, but could be quite useful for the right character and is good flavor. Decision should be made on the level of an RP choice.
Resistance to Pathogens/Toxins: If you're going to take this Quality, take it at the 10 BP level... Neither Pathogens nor Toxins have never been that commonly used against me at the tables I've played at, and Pathogens least, so if you have reason to believe you might use it more than once or twice in your campaign, you could consider taking this.
Toughness: 20 Karma for 1 physical soak box or 20 Karma for 1 physical box, damage resistance, more armor, and resistance to poisons and such, etc.? Don't take Toughness.
Will to Live: you know, I actually kind of like this Quality if you're a primary combatant and you pair it with Vasocon (Bioware/Genetech). More importantly though, I like this for a Missions-specific Primary Combatant - or for anyone who wants to hang onto their PC for as long as possible. I tend not to get too attached to my SR characters, but maybe that's because I've never taken this Quality?
Martial Arts: on their face, Martial Arts are essentially 10 Karma Posi Qualities that give you a +1 to a situational dice pool (Advantages). Whether it's to DV or various types of attacks or actions. Which at face value is actually kind of expensive, similar to the "+1 or 2 to X-Skill or Test(s)" Qualities that I generally recommend against. However, when you consider that these bonuses almost always stack and are often unattainable through any other method, Martial Arts clearly become a worthwhile expenditure of resources for a character who has melee fighting as primary aspect of their role. That said, melee combat is usually very situational and unless that's your PCs "thing" (like an Unarmed Adept), I would advise against investing too heavily in Martial Arts at Chargen - because you can pick them up during play, for no loss or gain in Karma over doing it at Chargen.
Furthermore, when we look at Maneuvers, we can compare them to Specializations, at Chargen (4 Karma). Maneuvers are best when used in synergistic organizations (i.e. combined with other Maneuvers, Advantages or Qualities), but can also be good RP elements. Some Maneuvers are better than others. In general, Maneuvers where you have to give up a successful attack (Clinch, Disorient, Herding, or Set-up) for a later bonus or other effect should be avoided (like the plague). Because of how combat works in Shadowrun, you want to apply that damage as soon as possible, whenever you have the chance - not more later, or for some effect on the following IP. Yes, even combining Set-up with Finishing Move isn't all it's cracked up to be, because if you choose to deal damage from the first attack, instead of Set-up, not only will the defender potentially have the damage modifiers from that, but they'll have -1 dice for already having defended against an attack. The exception being if your opponent is heavily armored and you'd need the extra successes to do anything to them at all, or if it's an RP-choices.
Many more Maneuvers border on RP-choices (Blind Fighting, Break Weapon, Ground Fighting, Sweep), because while their applications can be used effectively, they are such niche situations that the cost may not really make sense, even when considering the "Rule of Cool" that comes with them. And some are just poor choices (Evasion, Focus Will, and Vicious Blow), which no one should probably ever take.
That leaves us the alright ones (Full Offense, Multi-Strike, Off-hand Training) and the good ones (Disarm, Finishing Move, Iajutsu, Riposte, Throw, Two Weapon Style, and Watchful Guard). Many (if not all) of these recommendable Maneuvers are only recommendable when combined with other Maneuvers (or Advantages or Qualities). I'm not going to go into all of the combinations, you should either study them until they are apparent to you, or there are other threads which go into this at length.
Spells: these are, of course, the reason most players decide to make a Magician. Spirits are great (fantastic even), but who doesn't love a good face-melting? The one Karma-efficiency thing to note for Spells is that they are slightly cheaper after Chargen, than during (6 Karma vs. 5 Karma) - not really a big deal, but Magicians are always gonna be tight on BP, so you should try to take the minimal number of Spells that will give you the capabilities you want. For instance, taking your full 15 Spells at Chargen when you could do fine with just 10 is a whole post-Chargen Spell-worth of Karma, and that saved 15 BP saved is a good portion of that Force 4 Power Foci which if you buy now, will save you Karma down the road...
As with everything you do in your build, you should look for Synergy too, and Spells are a huge part of that for Magicians. If you are a Shaman, you should be able to easily dabble in Facing, if you're Hermetic you should be able to easily dabble in any of the multitude of LOG skills, especially First Aid and Medicine, but also B&E (Hardware) and sabotage skillsets (Demolitions, Mechanics, etc.). This Synergy should not only come from your Attributes, but also your Spells to buff those Attributes and augment those roles and skillsets.
Contacts: are probably the most under-valued and over-looked portion of Chargen. When BP runs tight, it's Contacts that get the axe. This is a shame, because Contacts should be more than just someone who hooks you up with Johnson, or whom you buy and sell things from and to, or whom you ask about X topic for their expertise. Especially if you're allowed to use Advanced Contact rules, Contacts should be integral parts to your PC who either cover your weaknesses or augment your strengths even further (ideally, both). With Group Contacts for just a few more Karma on top of what you might normally invest in a good Contact, you can have Magical and Matrix knowledge and capabilities just a 'link away.
Taking a Group Contact is a good way to avoid redundant Contacts too, like taking a Fixer and a Johnson, or a Bar Tender and a Blogger, or when you could have just replaced all of them with a well-Connected Hacker Group Contact. Bottom line get the most out of your Contact purchases; avoid Contacts with redundant functions.