Ralph,
I like your list, and not much to quibble (word fo teh day?) with off the top of my head.
Bracketgate game, you should mention, was a first-round matchup.
The D3football.com era begins in 1999 ... one thing you could mention, however, is that the MAC was South Region for much of this time, so maybe that squeaks someone like Widener 2000 into the top 10, or maybe you want only to include the current South Region teams.
I see you mostly have Stagg Bowl teams, regional champions and such on the list too. Probably wise.
The 66-0 Bridgewater team really wasn't that bad; that score (and it could've been 74-0, easy) was the result of schematic disaster that was actually rooted in a good idea. Bridgewater (built on speed, remember) would cover Mount Union receivers 1-on-1 so it could rush enough people to keep the Purple Raiders' QBs from sitting back and picking them apart. However, MUC seemed to pick up the blitzes, and the twin 6-foot-4 WRs made catches against Bridgewater's smaller CBs all day, and it got ugly in a hurry.
Definitely the 2001 Bridgewater team and the 2004 Mary Hardin-Baylor team are two of the best in a long time. I wouldn't beef with anyone who flipped the order there, although UMHB's road run was definitely the more impressive accomplishment, and the Rowan/Bwater semifinal too ... yeah, I'll agree with UMHB at No. 1, but that Lutz/Cruz, etc. team was a powerhouse.
I still think UMHB running the ball down 14 at MUC in the 4th quarter, and it working, was one of the most impressive things I've ever seen in D3 football. Had it not been for The Catch (immortalized on UMHB football building walls) though, I wouldn't remember it as such.
Just some ramblings to support your rankings, I suppose.