In no particular order:
Between the Lines (1977)
Behind the scenes of an underground Boston newspaper on the verge of being bought out. Great ensemble work by a then cast of unknows including Jeff Goldblum, John Heard, Bruno Kirby, Jill Eikenberry, Lindsay Crouse, etc.
Twice Upon a Time (1983)
Perhaps my favorite animated flick of all time. Done in the exclusive Lumage process (imagine a fully rounded version of the cutout work done by Gilliam), and the only animated film produced by George Lucas, it is an ascerbically funny little fantasy about the evil Synonamess Botch trying to fill the world with nightmares. Beautiful to watch, infinitely quotable ("Here's my resume. It's a blank piece of paper but it is legal-sized and notarized."), and containing great voice work. Released in two versions: a wider released PG version (found on subsequent video and LD releases) and a cruder, but funnier PG-13 to R version only seen in a handful of HBO showings back in the mid-80's. If possible, that is the version to see.
The Adventures of Mark Twain (1986)
The only feature film from the Will Vinton studios, a beautifully realized claymation fantasy based on Twain's writings. Its dark tone (it centers on Twain sailing to meet Haley's Comet upon its return so that he can die) does not make it entirely kid friendly. But in many ways, it is one of the truest adaptations of Twain's work out there (esp. the haunting sequences involving the Mysterious Stranger).
Ace in the Hole (aka The Big Carnival) (1951)
The forgotten Billy Wilder masterpiece, starring Kirk Douglas as a reporter milking a mining disaster story for every last ounce of ink he can squeeze out of it, irregardless of the cost to those involved. Shows on AMC from time to time...catch it if you can..its a real find.
Get Crazy (1983)
The funniest flick that no one has ever seen. From the mind of Allan Arkush ("Rock and Roll High School") and based on his years working at the Fillmore, it centers on the back stage going-ons ata New Year's concert. Great cast, including Malcolm McDowell in full Jagger mode, Lou Reed as a Dylan-like recluse, Ed Begley, Jr as the bad guy, Fabian and Bobby Sherman as his henchman, Daniel Stern, and a scene-stealing turn by Bill Henderson as King Blues. Again, infintely quotable ("Pardon me while I bask in my own genius.").
Other great overlooked gems:
I Go Pogo (aka Pogo for President) - Smart political satire wrapped in a kids claymation fest.
The Unbelievable Truth - Great debut from indie filmmmaker Hal Hartley. Probably his most accesible film.
The Ninth Configuration - Film written and directed by William Peter Blatty, centering around a hospital for mentally ill soldiers.
Lord Love a Duck - Another satire, this one from the 1960's starring Roddy Mcdowall as a nerd trying to fulfill the vapid dreams of the girl of his dreams (Tuesday Weld), irregardless of the cost.