Zombieland is a good example.
I highly, highly highly recommend that people see Moon. Relatively low-budget under the rade type of movie - Sam Shepard is great in it.
Get Him to the Greek. If you don't laugh at this movie, you're a drip. Ditto for Saving Sarah Marshall.
The Prestige. Kingdom of Heaven. The Assassination of Jesse James...(Sam Shepard, again.) Fallen. (Denzel Washington). Jacob's Ladder. Everything by Wes Anderson.
Barton Fink has always been one of my favorite movies. Hard to call any Coen brothers' underrated, but they might be so overrated that they come full circle to underrated. The Big Lebowski and O Brother Where Art Thou? are brilliant.
And, because I am the father of an elementary-school aged girl and she has been my most constant movie date over the past nine years, I might be an expert on animated films.
The Incredibles is supposed to be Pixar's best film. It's not - Finding Nemo is. I don't recall being crazy about it when it came out, but having seen it about 200 times with my daughter since, it's almost perfect. I can't say any other Pixar movies are really underrated - perhaps A Bug's Life. The rest are as good as their reps with the possible exception of Brave....wasn't crazy about it. Cars 2 stunk.
Arthur Christmas and Pirates! Band of Misfits are both very, very good.