Clean Install with Exceptions My current OS X install is getting long in the tooth. It's been ported over through multiple OS upgrades and system changes (started with an iMac G4, then a PowerMac G5, and now a iMac i7). 

I think it's about time to do a clean install to get rid of all the crap that's been accumulated. Is there a way to do a clean install with exceptions? I'd love to keep my applications and application preferences intact, but pretty much start anew with everything else. 

I've got Time Machine backups, and would do a SuperDuper copy to an external drive before starting fresh.
AFAIK Migration Assistant will let you do just what you've asked. Here is an article on this but it's pretty straightforward.