Oh boy!
What books do you have, and is your GM looking to get very in-depth with the matrix, or not?
There's a lot of intricacy here, and, I could spend 1000s of words going into it all.
Basically, you're going to want:
Stealth and Exploit to crack systems.
Spoof, Trace and a Sniffer to hijack drones and other devices.
Nuke and Attack for dealing with enemy hackers/IC or technomancers respectively and Medic to clean your icon up after a fight (and a Medkit attached to your arm for healing Black attacks via the Command prog.)
Defuse, because a Data Bomb can and will end your hack cold.
ECCM because it goes through walls. Wi-fi inhibiting walls.
Analyze, because it's your eyes.
Browse, because it's how you find things.
Edit, because it's how you hide your tracks.
Command because command allows you to use anything, and well.
Encrypt to slow down enemy hackers.
Scan, because it's how you find devices to hack.
Things that you might need:
Data Bomb, for keeping out enemy hackers. The most essential of the non-essential programs.
Black Hammer/Blackout, for when kicking someone out of the system just isn't enough.
Corrupt, for when you need to edit something in such a way that it can never be recovered again and when you can't even be bothered to find it first.
Things that you probably won't ever need:
Armor: 2-3 hits will generally crash you regardless of this little tiny bit of damage soak. You get crashed, flip to a new ID and hack back in.
Biofeedback filter: Same general thing as above. If you're in trouble, Run! A good Spoof program will break you free if your connection gets jammed open.
Disarm: If you've got time to Disarm, then you can generally edit yourself permissions or just Nuke the guy.
Purge: If you let a virus or trojan get on your computer, you have already erred significantly.
Reality Filter: Plus or minus one response on a die roll? Dumb. Evey node has your same metaphor? Dumb.
Advanced things for good times:
Negator, because it is so cheap and so perfect. It accomplishes what usually takes a continuous high-level edit action, specifically editing out any object in real time, and does so with no test. Automatically remove your entire team from the security feed as it streams. Hell, put it in someone's AR goggles or cybereyes and you can make them overlook any object you choose. Attach a corrupt tag and it will wipe itself out once its job has been done. No muss, no fuss, no record of your team in the security system. At 100 yen, it's a steal.
TacNet, because +1-4 on all Combat active skill tests and all Physical active skill tests which are associated with a mental attribute. It's really, really awesome, and fairly cheap to boot.