Yes, Richard D. James (Aphex Twin) is a bonafide genius.
It would be hard to say which of his works are my favorite, as it largely depends on my mood at any given time, but...
Some of my favorite tracks:
1. "We Are The Music Makers" (for the Willy Wonka reference, of course.

) from Selected Ambient Works 85-92
2. "Track #1" from Selected Ambient Works, Vol II. - so creepy, and yet so delightful!
3. "54 Cymru Beats" from Drukqs (plus "Lornaderek", the creepy Happy Birthday message from his weird, old parents, with the wraspy laughing and the thick British accents. Makes me think of a scene in some lost Stanley Kubrick film.)
4. Pretty much the whole Richard D. James Album, especially "Cornish Acid" and "Beetles".
5. pretty much the whole I Care Because You Do album, especially "Ventolin" and "Come on You Slags!"
6. Pretty much all of Classics
7. "Windowlicker", of course
8. "Come To Daddy", of course
9. "Polygon Window" from Surfing on Sine Waves.
10. "Donkey Rhubarb"
Plus, his videos are amazing - especially the ones directed by Chris Cunningham