Any video directed by Michel Gondry are tops in my book.
But traditionally, Daft Punk Around the World, and The Chemical Brothers Star Guitar.
Both videos have visual elements that represent the various instruments and sounds.
Around the World's choreography is absolutely brilliant. Every dancer represents an instrument, and has a dance steps that represents the notes! Crazy!
Star Guitar was a visual achievement when it came out due to the seamless stitching of visual landscapes that also represent instruments. But also the incredible thing about this video is the timing of when objects appear on camera, representing notes of the song. Every objects, be it a post, a building, a shrub, etc... are all spawned at the timing of the notes. It gets mesmerizing just seeing what thing represents what.
Other honorable Michel Gondry mentions:
Kylie Minogue "
Come Into My World" - awesome "parallel pathing" choreography editing
The White Stripes “
The Hardest Button to Button” - instrument duplication on the beat and rhythm (apparently they had to have a shit-ton of gear to make this video)