When I made the list I didn't just look at the overall rating I gave to the movies, I also took into account how much the time travel part contributed to how good the movie was. For example, I liked Twelve Monkeys a lot but not because there was time travel in it.
Top 5 Time Travel Movies
1. Back to the Future (1985)
Directed by: Robert Zemeckis
Genre: Sci-fi, Comedy
2. Frequency (2000)
Directed by: Gregory Hoblit
Genre: Sci-fi, Drama, Crime
3. Primer (2004)
Directed by: Shane Carruth
4. Los cronocrímenes (2007)
Directed by: Nacho Vigalondo
Genre: Sci-fi, Crime, Thriller
5. Midnight in Paris (2011)
Directed by: Woody Allen
Genre: Drama, Comedy
You all know Back to the Future. I normally don't like 80s comedies that much, but this one is an exception. Also, it does take time travel seriously and makes it funny without making it too silly.
Frequency is the first film to appear on a list for the second time. It's an interesting story about a son that by mistake contacts his father 30 years earlier on a radio.
Primer may be the movie in this list with the least plot holes and is also the most scientific one. It's a low budget movie that's quite hard to follow, but the story is well written and interesting. I'd say, use subtitles, it'll make it easier.
Los cronoscrimenes, or Timecrimes, has kind of the same theory about time travel as Primer, but focuses more on the story than the theory.
Midnight in Paris was a great movie, not about the science of time travel, but mostly about what you make out of the oppurtunity, which is kind of unusual.
For more recommendations:
Check out this thread: Time travel
Or this list: Time Travel Movies