An update, perhaps the final one.
We have finally figured out what is going on with Oreo. After two more of those growths appeared and grew, Oreo decided he didn't like them and ripped them off. Again.
After sending these lumps in for a biopsy, we got an answer to what these were. Turns out they're a bacterial infection-like thing called Bacterial Granuloma, and not a fungus at all. It's a genetic issue, a problem with Oreo himself. We can go in if it starts up again, and there are some things we can do to get it to fall out before it becomes too big, but there is no way to prevent it from happening in the first place. It hasn't been coming back for awhile though, so I'm hoping for the best!
Another gecko mentioned in this humungous thread, Spotty, has some problems though.
She was up in my brother's room, and he didn't feed her or hold her right and I ended up having to do everything. Since she wasn't downstairs with my other geckos, often times I wouldn't be able to feed her...she grew much too skinny for my liking. We moved her downstairs, and now she's getting food and good attention regularly. I did, however, notice something wrong with her back legs. Not going to go into too much detail, but our doctor thinks it's Lymphedema caused by a heart problem.
Wishing for the best!