Junebug
George Washington
Alice Doesn't Live Here Anymore (D. Martin Scorcese)
Before Sunset (D. Richard Linklater)
Time Bandits (D. Terry Gilliam)
Baron Munchausen (D. Terry Gilliam)
Heat (D. Michael Mann)
The Browning Version (D. )
Run, Lola, Run (D. Tom Tyvtner)
Matewan (D. John Sayles)
Tampopo (D. )
The Third Man (D. Carol Reed)
Working Girl (Nichols)
Not really "gems" but also sometimes overlooked:
The Apartment (D. Billy Wilder, 1961)
We know all about the star vehicles, and the classics, and the great films like "Dr. Strangelove" and "The Third Man" and "Seventh Seal", and the over-blown Hollywood blockbusters. How about a word for the "gems".
A "gem" is a relatively low-budget film that is quirky or charming or delightful-- usually better than expected-- and authentic in some unexpected way.
They are also often overlooked because they don't feature the big stars or budgets of the Hollywood extravaganza, nor the critical acclaim and awards of the critical establishment. They often have more personality though-- because the director and author, being much closer to the ground, have more control over the content and more of an opportunity to throw stuff in that tickles them.
Sometimes a gem receives such widespread, consistent recognition (like "12 Angry Men") that it no longer really qualifies as a gem: it moves into another category altogether, as a great film. Sometimes a great film-- like "The Third Man"-- continues to be overlooked in spite of both awards and acclaim, so I added it to the list.
The quintessential "gem" is "My Cousin Vinny". No, it's never going to be regarded as a great film or a classic. Watch it three times and the seams start to show. It's simply a very funny, fresh little film that doesn't apologize for starring Joe Pesci and Marisa Tomei.