Okay, I'm in a creative mood, so I'll try to come up with a few. They're obvious, but I hope my ideas would be of use to someone.
1. A shop. Obviously, this is a great cover, whether it would be a talismonger, or used electronics shop. Or even a pawn shop, or grocery. It would need some work, but still, having a legitimate, or semi-legitimate business cover would be great, especially if you register all the teammates as workers/owners. You can stash your gear in the basement, or attic, and have a living area, or just a bunk or two in the 'staff room'. Besides, if handled correctly it could be a steady and significant source of income, and you could easily use it for the 'Day Job' negative quality. It would be great if the whole team takes that one, and you'd have a full, reliable staff. Any other kinds of business should work too - even a medical clinic, cyberware parlor, machine shop. Anything you can fit in the frame above. And a few optional choices of safehouse qualities from Runner's Companion would be a nice addition. If you'd create it along with your characters, a few of them taking 'Day Job' would be enough to cover the bills (lifestyle cost for the entire team), and depending on how much time you'd have to spend (for example without any staff to hire), you could make it even a primary source of income. Or, on the other hand, that kind of a safehouse would be a great background for a high-end contact (with high Loyalty at least), like a fixer who uses the 'ordinary shop owner' act as a cover for his less ordinary business, and who's hiring your characters on both sides of his establishment.
Besides, that kind of facade would be a great opportunity to tune the safehouse security, but with care - nobody would take a grocery with killer drones and military-grade matrix security for normal.
2. A bar, or other kind of business like it - restaurant, hotel, etc. That's not exactly like the former, because it's a lot more public. But this can be turned to your advantage. If your characters are regulars, and they either work there, or know the owner/staff really good (like above, Day(or night) Job, or Contact(s), they can easily live there. On sythanol and krill wafers bar diet, or even having a 'on the house' policy on food, as long as they keep their end of the bargain (doing a good job, contact's loyalty). The owner doesn't even have to know what the characters dabble in. He can be a good friend, family member, or even an old acquaintance of theirs, who owes them enough to let use his business as a safehouse. The public nature of the place would be both good and bad. Good, because you could easily hide in the crowd, or meet the people you need. Bad, because there are always eyes and ears in the public. And because the owner would be in trouble if the characters are on the run.
3. A house. Seriously, the usual regular apartment, or penthouse would serve as a great safehouse. Especially if it's not used all the time. If your characters just buy and secure one, you can always put one of your friendly NPC's or even contacts in it, to serve as both caretaker, and cover. Or they might crash at one of their teammates family members, sensei, or lover. The security would be a problem, but it's nothing they couldn't fine-tune. Or, the place itself could be on corporate ground - for example, on S-K property, if they never, ever would run against the dragon. Or deep in gang territory, on a highly private housing area, or even tribal lands.
4. Squatting. Yeah, it's covered in the rulebooks already. But with enough money and time one could turn a half-ruined church, or an old power station into a private little heaven, with stolen (or half-legally acquired), or improvised water, electricity and matrix. The amount of places that can be used for this kind of a safehouse is huge. From severs, to old military outposts, every place can be turned into a comfy little fortress, and supplied with all you want for your alter egos. For example:
Your characters decide to take over an old fire station. They have a small, two-story building with a huge garage space and basement. Enough for the rigger's workshop and drones, magicians lodge, an armory for the samurai, and even training room for the adept, and a server room for the hacker. You just find a way to repair it, supply it with power, water and matrix coverage, and all the luxury and equipment you need, and then apply security. And bam! - you have a home sweet home.
It could even be a full-fledged campaign objective - turn the fire-house into a luxury-fortress. With runs to either get the money, or pay for stuff with favors.
Damn, I'd play in a game like this...
