I second
Dead Leaves - high paced brilliant over the top anime
Primer - Genius script and it shows that anyone can make an entertaining movie, I think the budget was $7000,- or something like that
Eraser - especially the usage of sound makes this an enjoyable nightmarish trip
Bubba Ho Tep - When the are they going to start film Bubba Nosferatu
Was surprised to actually see Surf nazis must die mentioned here, for a long time I regarded that as one of the worst movies ever. Maybe if I can see it again I can laugh about it.
Weird noone has mentioned Harmony Korine, I think Kids sucks however Gummo is a must see as is Julien Donkey Boy. 2 Of my favourite movies
Also C'est arrivé prés de chez vous (known as man bites dog) its a film about a low budget documentary team following a serial killer and filming his exploits, highly recommended.
And for fun and for the sole reason that you can say that you have watched it : Gayniggers from Outer Space
It even has an IMDB entry