So I spent most of last Saturday night figuring out the header information inside of GameBoy ROMs. Basically, games such as Pokemon Stadium check the header for information regarding what game is actually present in the transfer pak. The end goal of this quest was to get ROM hacks working on both Pokemon Stadium 1 and 2 as any OEM Pokemon game would.
It was a success! I found out that by coping the header from a stock ROM you can play ROM hacks on both Pokemon Stadium 1 and 2. Interestingly enough, games are also region locked. I tried my physical copy of the Japanese games on an English copy of Pokemon Stadium, and they are not recognized. Same goes for the other way around. By changing one hex value in the header, you can make the game think that the cartridge inside is an NTSC ROM and it'll read and play just the same.
For example, I dumped my Pocket Monsters Midori ROM from the cartridge. Pokemon Stadium still has the SGB frame for Pokemon Green, even though the game never saw an English release which I thought was kind of neat.
So, aside from the ramblings above, essentially what I have is a way to get ROM hacks to play the same as OEM games on Pokemon Stadium. The easiest way to do it that I have found is to copy the header from whatever the base game was for the hack. For Pokemon Prism, you'd use the Pokemon Crystal header. Pokemon Red++ uses Red and etc. The coolest thing is that if the hack isn't fundamentally different (for exmaple, Red ++ added extra Pokemon so it wouldn't work with that hack) you can still transfer Pokemon and use things like Prof. Oak's lab and such in Pokemon Stadium 2.
Even though most of the Pokemon Stadium features are locked specifically to the Pokemon games only, you can still use the header editing to play other games through the transfer pak. Basically, as long as you make the header any Pokemon game that is normally playable in the GB Tower, ANY GameBoy game will work.
I'll be writing a PC program to do this automatically for any ROM. The plan is to allow users to pick any of the 6 headers from the english releases and any of the 7 Japanese releases and apply it to the ROM of your choice so that you can use these carts to play games on the GB Tower.