Thanks for the tip. It's clear the scrubbing tools I used were faulty so I'm building a redump GameCube collection and using WIT to scrub them. WIT seems to work well, for example it doesn't erase the Simpsons FMVs. I'm keeping the redump versions also to be safe. So far I've processed the first two letters and am now halfway through the B's.
Fow Wii games I'm favoring wbfs files. It seems to have the widest support and my only complaint is that it's limited to 4GB. Storing them as 7z files with LZMA2 squeezes a few extra MB out. I've avoided LZMA2 in the past since it's so new but I think it's time to give it a shot. Redump doesn't have Wii yet and I've found few sites with a decent library, so it's moving slowly.