Okay, here's a tip: When you go to get the Reaper IFF, that kicks off the endgame. If you want the best ending, you can only do one or two missions after getting the IFF, and one of those needs to be Legion's loyalty mission.
Basically, before getting the IFF, make sure you've finished all your crew member's loyalty missions. If you don't they will likely die in the suicide mission.
Also, there is only one way to make sure Mordin survives to the ending. This may not make sense now, but remember it for the final mission: Have Mordin accompany the crew. Otherwise he's a goner.
SPOILERS IN THIS COMMENT I'M SERIOUS GALS
Basically, before getting the IFF, make sure you've finished all your crew member's loyalty missions. If you don't they will likely die in the suicide mission.
Also, there is only one way to make sure Mordin survives to the ending. This may not make sense now, but remember it for the final mission: Have Mordin accompany the crew. Otherwise he's a goner.