I pretty much like all the ones I've seen, so:

Cloverfield (2008) A clever use of the found footage theme, where it's all taken from one camera, displayed as-is, but a plot point is that the cameraman himself has overwritten older footage on the tape with newer footage, so you get bits and pieces of what was previously on the tape.

Jacob's Ladder (1990) The main storyline is intercut with flashbacks to Vietnam, and there's a particularly lengthy sequence where Jacob's son is alive (after it's been established he's dead) and he's still with his wife (who he divorced), which makes you question everything you've been seeing so far, and what's a dream and what isn't. Semi-fits into the category of non-lineary narratives, though to say more would invoke spoilers.

Kill Bill. Vol 1 (2003) & 2 (2004) Of course like almost any Tarantino movie, he plays with the timeline. Nothing more needs to be said. It's Tarantino. It's fun.

The Machinist (2004) Similar to Jacob's Ladder in many respects, the main character thinks he's going crazy, though this one doesn't play with time so much as it does withhold a vital flashback scene until the end. However, the opening sequence is interesting because without context, you quickly forget about it, but then it is repeated later in the movie and you get a sense of deja vu. If you like this, you may also like Stay (2005), also not strictly having a non-linear narrative, but of the same vein as The Machinist & Jacob's Ladder.

Reservoir Dogs (1992) Another Tarantino. Awesome as usual.