I kept everyone alive except... Mordin. Dammit, I really liked him. Bioware, you guys are cruel. I think the only questionable decision I made was sending back Zaeed to escort Dr. Chakwas; my theory was that if one single person is going to be escorting a noncombatant through an alien base full of heavily armed monsters, it'd better be someone who is a walking army, but perhaps having him in the rear-guard action at the end would have worked out better.
I don't know if I want to try and replay the last section of the game and/or the ending or not. So far, I've pretty much stuck with whatever decisions I made during both ME 1 and 2, rather than replaying when something didn't go according to plan. But, y'know, I feel pretty bad about the entire crew getting lost -- my understanding is that if you want to save any lives you have to hit the Collector base as soon as they're taken, but I thought it would be better to finish all the loyalty quests first. There were four of them, though, and when I finally got to the base, everyone except Chakwas was slurry.
(But -- Whoa. I just remembered that my Commander Shepard has the "Colonist" and "Sole Survivor" backgrounds. In both of which she was the only survivor of some random horror that destroyed first her home colony and then her military unit. And now this happens... Dang. It's depressing but I have to admit it's completely in character. I kind of hope I'm not stuck with a lonely, quiet Normandy in the third game if I go with this, though.)
(Then again, it would also be completely in character to say "never again" and save everyone, even if it means breaking the laws of time and space and looking up a few hints on the Mass Effect Wiki. Upon further research, it looks like I've got a save from right after collecting the Reaper IFF; all I'd have to do is Legion's quest, then I can still go through the relay and get the best ending with the characters I have.)
The other major decision you get to make at the end is when the Illusive Man calls up and suggests that instead of blowing up the Reaper factory, you should instead disable it so humanity can use the technology in the base to defend itself against the expected all-out Reaper attack. And yeah, maybe that seems sensible. But, y'know, I can't count how many times in ME 1 and 2 I've answered a distress signal to find a base full of zombies and a series of recorded log messages that start with "Hey we found this awesome alien technology, we're going to turn it on right now" and end with "BLARAREREARRRGHGHLLLL." So instead I told him to go to hell and blew the place to smithereens. It was especially satisfying as I'd brought Miranda along on the mission and she quit too, right to his face. Hey, Illusive Man, you hire someone as tediously noble as my Shepard, you should have expected something like this to happen in the end.
Final note: During the New Game+ I was finally able to ask Legion what the deal was with that piece of N7 armor he (it? they?) was wearing. Wow, that was a weird conversation. "No data available"... the way he said it at the end gives me the shivers.