I find it a little unsettling that so many of you guys seem to be conflating "old movies that are good" with "ahead of their time," as if good movies are a recent invention. Anyway, a couple off the top of my head:
Zero for Conduct (Vigo, 1933) - An anarchic punk rock movie made decades before rock 'n roll itself even existed, a French New Wave film made before most New Wave directors were potty-trained, a movie that was banned for over a decade after it was released.
Sherlock, Jr. and The General (Keaton, 1924 and 1926) - Both poorly received at the time of their release, both incalculably huge influences on both comedy and action movies. Plus Sherlock, Jr. gets amazingly meta for a silent film from the '20s.
Sunrise: A Song of Two Humans (Murnau, 1927) - Murnau's camera swoops and glides while most of his contemporaries' cameras were just learning to walk.
Citizen Kane (Welles, 1941) - Duh. The deep compositions, the fragmented narrative, the low-key lighting, the low-angle shots, plus lots of people don't realize that Kane is actually a landmark special effects movie too. There's a reason why this is the most frequently cited "most influential movie of all time" and there's a reason why few people felt that way at the time of its release.
Johnny Guitar (Ray, 1954). A feminist lesbian psychosexual revisionist Western. From fucking 1954.