I bet there's more than 100 "S" games. Search results are capped at 100 so it sounds like I need to tweak that. I'll get it fixed later today. As for Spider-Man, my manual uploader kept the submitted filename and all pages in The Manual Project (and the Vault) alphebetize by filename. So, when someone submits a Spider-Man game as "MaximumCarnage" it gets shown with the M's. The new system I've designed makes you select your game from the list if it's a system in the Vault, otherwise it will generate a filename based on the title you enter. So, assuming the submitter knows the title of their manual it will show up in the right place. I'll try to finish the uploader this weekend. It's about time I got it working again.
Ok, they are not gone, because they can be found if you search for them by name, they are just missing when you look at the "S" list.