In no particular order:
1. X-men/Uncanny X-men First Class

I had no interest in picking up X-men First Class. None. I didn't give a crap about the O5, and honestly I disliked most of them (Cyke and Beast, DIAF). However, in doing image searches here and there for whatever I was posting on CBR, I kept coming across these amazing panels from the book. I finally picked it up, and words cannot describe how wonderful it is. It's a beautifully written introduction to the X-men, by a guy who clearly loves them and knows what he's doing. Parker is magical on this book, and it's fun, lighthearted, and exciting. And the Colleen Coover stories in between are fabulous. Jean and Wanda going shopping and getting bugged by Pietro, the Professor screwing with the kids when they play on the Ouija board, Jean tracking a family of ducklings. I don't know what else to say except pick it up.
And I bundle in Uncanny here, because it involves the Giant Sized, which of course means Nightcrawler, and is every bit as amazing. Go get it!
2. X-Force/X-Statix

I have NO idea why this book is no longer being written. I suppose I do, but it's a shame. It takes the whole mutant superhero concept and turns it on it's head. The X-men are persecuted, and yet they trudge on to save a world that hates them. X-Force, and later X-Statix, capitalize on that. They're in it for the money, plain and simple. They're celebrities, the have agents, they don't fight unless there's something to be gained. It's human nature played out in the pages. There are those who do for others, and there are those who do for others when others are sure to be watching. X-Statix are the latter. That's not to say they don't evolve and grow. They don't stay so shallow, but the heart of the team does. It's about fame and glamour, saving the world is second. Some of my favorite characters come from the pages of X-Statix - U Go Girl, for one. I highly recommend giving these a read. At very least, it's a ton of fun.
3. Exiles

This should come as a surprise to no one. Exiles was - dare I say it - THE best book of the past decade when under the care of Judd Winick. Hands down. NOTHING comes close. I may be biased, as my girl Nocturne was born and raised in that book, however it is that book that made me love her. Winick handled that book with a care that you don't see everywhere else. He was able to write storylines that lasted months, or years, that you never even realized were being set up until the last minute. He wrote about progressive subjects - gays, abortion, etc - without being heavy handed or making any grand social statement. It simply was. These are hero's who are living a life that shouldn't exist, and this is how that effects them. Not "this is happening and OMG!" "This is happening and this is how these people cope." Amazing. The book was ALL about the characters, completely run by characterization, and everything else came secondary. Just in the case of my girl and her abortion, the effects of losing John and her decision to abort their baby lasted in the books for over 10 ISSUES. And it wasn't in your face. But it was there, and it was clear. I can go ON about this book forever, but I'm just gonna say this: Read until you see Bedard's name. If you decide to keep going, stop before Claremont. Or you will regret ever picking it up.
What're your top X-books of the 2000's? Or if you haven't been reading lately, of all time?
[Edited on 31/8/11 by NachtcGleiskette]