A short list:
Harakiri - GREATEST MOVIE EVER MADE. See it on hulu.com - you can get a free trial subscription there.
Ride With the Devil - the studio torpedoed their own movie... due to concerns that no one who had actually *seen* the movie would have had. Watch this and you'll get a glimpse of many now-famous actors of today before they were "stars".
The Ice Harvest - Strippers. Booze. Gangsters. Mid-Life Crises. Christmas. IMHO, this very dark & dry comedy is better than Fargo, but was almost universally panned by the critics.
X - the Shakespearean Spike Lee Malcom X biopic - a great movie of redemption, faith, injustice, intrigue, zealotry, and betrayal. Denzel Washington gives one of the greatest acting performances of all time.
Alexander - Oliver Stone's Alexander of Macedon biopic. Had its weaknesses, and was almost universally panned by the criticocracy. But I think the 'ultimate' cut is a truly great movie (and as historical epics go, pretty damned accurate). The one shot of Alexander's horse and King Porrus' Elephant facing each other at Hydaspes and both rearing up on their hind legs is IMHO one of the most incredible images in the history of film (and, so Stone claims, completely unplanned). The Phillip/Alexander father/son relationship is both endearing and heartbreaking - Val Kilmer is one of the most underrated and underutilized actors of all time.
1492 - Ridley Scott's Chris Columbus biopic. Incredible images, a justly celebrated soundtrack by Vangelis. The critics hated it, though - perhaps poisoned by that *other* Columbus movie (nameless here, forever more...) that year which was truly terrible. And Gerard Depardieu's hideous accent was hard to understand. But I completely fail to understand why this movie has never been released on DVD/Blu-ray.
Kingdom of Heaven - The theatrical version truly sucked (due in large part to casting a no-talent pretty boy in the starring role). But the director's cut is a great film - see it just for the first act to see how truly grim medieval life could be in northern-ish Europe, and why people would be eager to go fight people they'd never met thousands of miles away for a land they'd never seen.