Aphex Twin's "Windowlicker" is one of his strongest pieces of music and my favorite music video. Besides the way the editing and physical movements of the participants and the camera's framing of those movements complement and reinforce the threateningly propulsive yet lasciviously slithery music, the video succeeds at being both hilarious and unsettling and takes mainstream R&B and hip hop videos of the period to their logical conclusion. Nice work, people.
Honorable mention: Built to Spill - "Carry the Zero"
I'm a sucker for melancholy guitar weepers that combine the post-punk and classic rock traditions, and this one does it better than most.