You mean someone besides me is actually interested? *does happy dance*
Anyway, I was thinking more along the lines of Earthside, at least for the most part. Maybe an AU where The Trust never becomes an issue because a less corrupt faction, the black-ops organization in question, realizes what's going on and stops the threat before it gets out of hand. That does of course mean that they have access to everything the The Trust did... So gate travel would be a distinct possibility.
Maybe they're in the pay of some other government (Say the Egyptian government. If one archaeologist can figure it out it's not outside of the realms for another to have.) as an insurance policy in case the shit really hits the fan, or something like that.
Another thought that I have is along the lines of more spy type stuffs with a few people actually working inside the SGC, and an organization trying to get their hooks in by cultivating those people as assets... But that could get really complicated and possibly boring unless you're into vast amounts of character development and mind games...
I'll think on it and see what else I can come up with, any thoughts that anyone else has are certainly welcome too. Oh, and I'm definitely thinking SG-1. I don't have anything against the other two, but SG-1 will always be my favorite.