Most everywhere I have seen his middle name as Gene, but one place I also saw it as Theodore (also John's middle name). However, I saw this online.

What do you do now, as a result of widespread internet access, that you didn't do ten years ago?

Mike Malinin: Easily find every book and CD that I want. Also read a bunch of incorrect info about myself, such as the fact that my middle name is "Gene" and that I used to be in Minor Threat. Although I wish that were true

So, I don't really know.