I just bought a used 2001 4Runner Sport Edition. The Dealership could only cough up one remote. I bought two more off Ebay for a song and now need to program them. Anyone know the process and save me an hour drive each way to the dealer?

Try http://www.4runners.org/articles/rs3000/

This is for a 98, but they are the same generation and it may well give you what you need. I found the pdf owner's manual (for the remote) extremely helpful.

Good luck!