It's hard to narrow it down to 3, but here goes, in no particular order:
Donnie Darko
Fight Club
Zodiac
Near misses for Seven, No Country For Old Men, Hot Fuzz, Dark Knight, The Matrix.
There are some interesting choices on here - Frank, although it didn't make your three, Seven was made in 95.
I would go for:
Amelie
No Country For Old Men
Big Fish
Very close up, Ratatouille, Little Miss Sunshine, Donnie Darko, Pans Labyrinth, Zodiac.
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