I'm interested in some cryptosystems that have been on the receiving end of any of these critiques that were ultimately shown to be sound and useful.

I'm not asking because I think I know the answer. I don't. I don't follow crypto the way you follow crypto; I am interested in it exclusively to the extent that it allows me to break software. You seem to follow the community as a whole, which is not an interest I share. So you probably have some insight into it that I lack.