Having just gotten an Intel Core Duo Mac Mini, I've run across a few applications that are indispensable: 
 
Intel compatible version of Firefox: 
 
http://wiki.mozilla.org/Mac:Intel 
 
TrimTheFat- This application will remove the PPC binary code from your universal applications. I pulled over 20 megabytes of code out of Apple's Mail program. 
 
http://www.versiontracker.com/dyn/moreinfo/macosx/28882 
 
I will continue to update this blog entry as more apps come to my attention.