back in july, i ran the dynasty list stuff i do from time to time, and it included conference dynasties. at that time, acc-crum was the #1 conference in d1, so that supports what zags was saying.
(current conf dynasty list link)
all time, there are a few special conferences.
(all time conf dynasty list link)
by huge margins, ACC-allen holds the top spot for 5, 10, 20, 30, and 40 years, in all of d1. they have the 1 year too but i just did that for fun to see single seasons, obviously 1 season doesn't mean a lot to being a dynasty. i think it is fair to call ACC-allen the gold standard.
in d2, there are two conferences that really set themselves apart. the GLV-tark has been one of the top 2-3 conferences in d2 for like 6+ years, and was easily #1 for like half of that. they hold top spots in 30/40 year dynasties, the latter by a huge margin.
in d2, there is also the Gulf South-allen, which had a really good run. they hold the top spot in the 5, 10, and 20 season dynasty lists, by a tiny margin, over the GLV-tark in all cases. comparing the two is interesting. Gulf South was great for a shorter time, in seasons and years, but the 1/day vs 2/day does make it harder for them to compete in the really long terms when measured in seasons. on the other hand, when the projection report came out, it became WAY easier for dominant conferences, numbers were inflated in a big way (getting 9 teams into the NT was as easy as 6 prior to the proj report, roughly). arguably, the best GLV run was before that change, so its pretty much impossible to say who peaked higher. i am obviously biased having spent 5 years or so in the GLV but because they are a VERY close second in the 5/10/20, a small to medium leader in 30, and huge in 40, and with their pre-new engine resume being easily the best of that time, i put them first. but i can certainly see a case for the Gulf South, as well. either way, both are easily among the game's all time great conferences.
d3 is a lot harder, because in terms of a clear leader, its harder. i wasn't involved in any of those conferences, I was in a top 30 all time d3 conference, but that's as close as i got. so, i never watched that closely. check the all-time dynasty list if you want to get some more info, but basically, there were a few dominant conferences over time. upstate-wooden was the gold standard for a long time - and they are really unfairly represented in the list - as mentioned, "old school" conferences get the shaft because it was SO much harder to send dominant numbers of teams to the NT back then. for example, in the GLV, our conference went down by all accounts, in strength, and we went from putting 6 guys in to 10, even with that drop. obviously, the heavy weights carry more weight, but even there guys who did well but lost games to several top 10 teams in conference, who would get 2-3 seeds today and 6 seeds back then. its really incomparable. so, i think wooden-upstate definitely deserves some credit despite "only" being like 5th or 6th on the dynasty lists. they are in contention for the best ever d3 conf in my book. there are like 4-5 other big time great d3 conferences you can see there in the dynasty lists.
it is a bit unfair to d1 confs, because they are behind the best conference ever, but really there were plenty of exceptional d1 conferences over time - generally d1 competition is higher, top to bottom, than d2/d3 (which are often roughly as competitive at the top, but not close in the middle/bottom). so when you see those top 10-20 d1 conferences, those were really GREAT conferences. also, as mentioned, old-time conferences get a huge shaft in numbers. i don't know when the projection report came out, its been a number of years now. you can see some great old-time conferences from some old dynasty list numbers i ran. the first conference dynasty list i ever ran was back in 2010 which either pre-dates the projection report, or is at worst right after it came out (i think it pre-dates it). if you care to look, you can see the list of dynasty lists i've compiled
over time here.