I've ran some Ad-Aware scans a while back, and they detected that I had some malware, worms and viruses. I allowed Ad-Aware to quarantine the files that it detected to be infected.

Now my question is....What should I do about the quarantined files if I want to un-install Ad-Aware? Should I restore the quarantined files before un-installing the software, or do I just un-install the program without doing anything to the quarantined files?

Hi
as long as you don't know for what these files are needed - restore them.
Install another software , start a scan and quarantine them again.
Regards
Raziel