I myself have dealt with this situation over the last few years, recovering just under 4 TB of archives from CD's and DVD's on a G5 Mac. One backup set, contained 461 CD's. Basically, I set the recoveries going, with what parameters I could bring into play, and fed Retrospect 6 the disks as it requested them. I stopped when I needed to, marked disks already recovered "missing" and started again, usually the next day.
It's a PITA, but it's part of your job if you're responsible for archiving data. No organization at this time should be depending on tapes or optical disks for archiving purposes--the media just aren't reliable enough. If you are responsible for maintaining an archive of any kind you must be prepared to migrate to newer media from time to time. In fact, you should plan on it.