I'm not sure how underappreciated it is (I still catch myself quoting it 22 years later) but it's one of those films that never seemed to get replayed a thousand times a week on cable. Maybe more of a cult classic than underappreciated, esp. among "90s kids."

In the same genre, more or less, Hackers.

Also, Kids, but different genre.

Unless you hung out with a lot of stoners, Dazed and Confused is probably underappreciated.

Night of the Comet, my first zombie movie, was replayed a thousand times a week on cable, but still good.

Serenity, the Firefly movie, is underappreciated by pretty much everyone who didn't love Firefly, but it works very well on its own (or so the few people who've seen the movie but not the tv show tell me.)

Black Dynamite, but that's a bit more appropriately appricated thanks to youtube.

Joe Versus the Volcano. Tom Hanks, three different Meg Ryans, and a definitive statement on the value of quality luggage.

The Fifth Element and Leon. Appreciated enough for most, but Fifth Element is in my top five films of all time, Luc Besson is in the top five auteurs list, and for my money the two best "comedic" performances by Gary Oldman. Speaking of Oldman..

JFK. Up there with Malcolm X and Schindler's on the 3+ hour list.