I have all my bonus feature stuff stored in a couple of six disc Amarays with sticky notes for labels, though I don't think I have near the quantity you have. My LD transfers of each of the OUT have their own cases with covers. I think I have a copy of the Holiday Special with its own case and cover floating around somewhere too. So, that gives me a total of 2 six disc cases and 4 one disc cases. Those six disc Amaray cases are pretty nice, I'd recommend going with those.

A CD wallet isn't a bad idea, but no matter what the packaging claims, it WILL scratch your discs. A spindle, though awkward and not too attractive on the shelf, not to mention inconvenient when you want access to a disc toward the bottom, is a pretty decent, cheap, and safe way of storing discs.