I'm doing something of a rewatch at the moment, and it occurs to me that there are quite a few plots that they have never gone back to. Me and Angel..er..Crichton Kicks that is, have been discussing the Re'tu on another thread. They looked like they had loads of potential as a major villain, but never appeared again (despite being a bit of a rip off of the shadows).
Another one that I'd like to see is what happened to Nicholas Ballard? They left him on that planet and never went back. He could well be dead by now.
Any other plots that have simply petered out, but could be revived now that the Go'a'uld are gone?
After watching A Hundred Days, i always wondered if Jack went back to Edora to see Laira. He uses it as an excuse when undercover in the next ep, but just gates to another planet.
Also we haven't seen Jonas since Fallout, i wonder what else is going on with him. We haven't heard much from the nox recently either.
Can't think of anymore, but i've found a lot of stories continued as fanfics.
Ems :)
Actually, I was wondering whatever happened to Marty? Given what was said in Citizen Joe I'm wondering what's he's doing now :)
Then of course there are the Aschen (from 2010 and 2001) - presumably some of them survived the various nasty addresses the SGC gave them in 2001, and I should think they're mightily pissed off with us now :)