I got a random command prompt popup when installing either planescape torment, or might and magic 2. I was able to read weiUD or something before it dissappeared. Can anyone confirm that this is normal? Cause I just redid my OS because of an infection i got trying to fix someone elses pc.

It's normal. It's installing patches.

Just to elaborate, it is a mod being installed. The name is weidu, it will crop up with any infinity engine game. Website:
http://weidu.org/
Welcome to the world of modding :o)

I didnt install any mods tho. Just the game.

I would assume that weidu is installed by default by GOG.

Indeed, its likely a widescreen mod, or possibly unfinished business mod.

Or fixes quests that would otherwise be game breaking? (This assumes they can't modify a file that's given and have to preserve it, but after it's installed it's not technically modified?)

Reminds me.. I'd love to see GoG start talking about some of the older games, the problems and solutions for compatibility they had to do, and why they made certain decisions.

While that was a wonderful read, it's way too generalized. I was thinking a game by game basis.

Say for example you had a lot of issues getting, oh say Albion to run, any issues with CD checks or files or music that played, what you experimented and found DosBox settings to work best, DRM you found or hidden easter eggs, or a glitch in emulation that made the game impossible to beat, etc. Sorta a rundown of a week by week and more in depth fixes and even code examples of what you had to change in the executable, including newer code that doesn't exist in 286 days, etc.

Thanks for the nice read!