The two most underrated movies of all time that had minimal theatre presence, but got all of their success from DVD and Cable are the Big Lebowski and Office Space. Two of the greatest comedies of all time without stupid frat boy humor that TRIES too hard like The Hangover. A few others in other genres:
Carlito's Way - Al Pacino as Cuban mobster trying to turn his life around with a great ending.
Quiz Show - Good little flick about a guy who is given the answers beforehand on a popular TV Game Show in the 1950s to generate ratings for the show and the investigation that follows. Nothing groundbreaking or special, just a good little flick.
The Game - Action/thriller with Michael Douglas that keeps you guessing what the hell is going on with a twist ending.
Just Friends - If your girl ever wants to stay home and watch a semi chick flick, pop this one in. Ryan Reynolds from Van Wilder is pretty funny here along with the chick from all of the Scary Movies. Van Wilder used to be a fat kid in high school that had a major crush on his hottie best friend/cocktease. When he's all grown up, he drops all of the weight and becomes a big time Hollywood producer, turns into a smooth dude, visits back home, and she becomes his kryptonite again.
The Mothman Prophecies - Richard Gere in this one, based on a true story. It's a haunting movie that isnt a bunch of cheap thrills with BS scare tactics.
City of God - Unfortunately, this movie needs subtitles, but it's basically Brazilian kids that grow up and become drug lords. Some of the characters remind me of the bad brother from Slumdog Millionaire. This film is hardcore.