In Absentia is probably the best place to start. Of their albums that I've heard, I consider Deadwing to be their best overall, but In Absentia has more stand-out tracks.
A lot of people love Fear of a Blank Planet, but I'm very lukewarm on it - although I will say that Sleep Together is one of the coolest songs ever.
Pre - In Absentia PT is very much a mixed bag. Seriously, there was a big leap in quality between that and their previous work. Stupid Dream is a good album though.
Haven't heard their latest, The Incident, so I can't comment on that.
Overall, they're an awesome band. A bit overrated, but great nonetheless. Sort of a Pink Floyd for our times, or a least as close as we're likely to get.