And if you unzip the ROMs, the files need to be in their own folders with the same name as the zip file, anyway.
I say keep them zipped, though. (Depending on the CPU speed vs the harddrive speed) Many modern computers can load and unzip a zip file faster than loading the same files (as in the zip file) unzipped on the same harddrive. Plus the disk space you save, CMPro, and copying/backing up, why unzip? *shrug*