Most of these I don't "hate" the original, but find the remixes far surperior IMO:

Otha Fish - The Pharcyde (LA Jay Remix)
Remember We - Bush Babees (Salaam Remi Remix)
Get Down - Craig Mack (Q-Tip Remix)
Lyrics - Special Ed (Buckwild Remix)
Mad Izm - Channel Live (Buckwild Remix)
You Can't Stop the Prophet - Jeru the Damaja (Pete Rock Remix)
The Ultimate - Artifacts (both Showbiz and Dilla remixes)
I Got a Love - Pete Rock & CL Smooth
Stress - Organized Konfusion (Extra P Remix)
Resurrection - Common (Extra P Remix)

outside of the 90s

As Serious As Your Life - Four Tet (Dilla remix)
Ether - Nas (9th Wonder remix)
Threat - Jay Z (Kev Brown remix)

all I can think of off the top...