Let me think. In recent memory:
Batman Begins (which I like, but its not the second coming)
A History Of Violence (which I also really liked, but again, I didnt think it was the masterpiece it was hyped as)
The Two Towers and The Return of the King (both of which have a ton of issues, and neither one of which is remotely as good as Fellowship)
Munich (Im not even sure what I expected from this one, but the film sure wasn't it. I loved Spielberg's direction and style, but the whole affair left me cold)
Im sure I could come up with tons more examples, but those are a few. Of course, then there is the opposite case, when a movie pleasantly surprises you.
EDIT: I forget the big one: King Kong (I kept hearing all this shit about it being a masterpiece, and PJ's best film, and when I saw it, I thought it was bar none the biggest turd I saw in 2005)