From this comment from this 2009 doomworld forums thread:

It was an in-joke, and don’t feel bad for not understanding it completely… I don’t really get it either :P

If you were wondering just in case of writing a story or some such, I doubt anyone would care if you re-define what the letters AGM mean.

In 2017, an issue has been open on GitHub, and a related freedoom forum thread was started with a poll.

Someone has then proposed a back story in 2018, in a separate doomworld forum thread, calling it

Advanced General Mechanics

Finally, last year, a new doomworld forum thread asked the age old question once again.

Personally, however, I would give it the meaning:

###Applied Genetics Manufacturing

(I also thought of “Apex Genetics…”, but I dunno, it sounds more sci-fi, but also a lot more gaudy)

Edit: funny enough, the domain agm.earth is available to purchase, and isn’t even prohibitively expensive (USD 30.36 to register and renew).