I'm assuming you mean the ones in the Sonic 3 part of S3&K on the Genesis. If this is the case, then there are only two changed tracks.
If you're referring to the PC port of S3&K, then there are MANY more tracks, such as:
Carnival Night 1: Genesis vs PC
Carnival Night 2: Genesis vs PC
Competition Theme: Genesis vs PC
Sonic 3 Credits: Genesis vs PC
It's never been officially stated why so many tracks were changed for the PC release, however, many people believe that it was due to Michael Jackson wishing not to be credited for working on Sonic 3, with the ensuing contract disputes causing Sega to create completely new tracks for every song Jackson worked on.
Hope this helps you out!