Off the top of my head, the best mid-major teams (idk if they're all undefeated, but they had great seasons):
'75 Arizona State.....WAC champs, had several top-10 seasons in the 70s, helping them join the Pac-8.
'83 BYU....was definitely better than the '84 NCs.
'85 Air Force....idk anything about this team, but a lot of ppl order it for the Whoa Nellie game
'90 BYU beat #1 Miami, but didn't have a great season
East Carolina had a big year in 1991
In addition to '04 and '08, Utah had a strong year in '94.
BYU went 14-1 in '96.
1998 was the Tulane year with Shaun King at QB.
I wouldn't put the Marshall teams of the last 90s in here, I believe their best win was vs a .500 WV team.
03 Miami-OH with Big Ben was a top 10 team, I believe
'07 Hawai'i was good until they played a big-boy team.
The more recent ones are jumbled up in my mind - the year TCU went undefeated, Boise State had a few, too.
Lousiville had a 13-1 team that was legit - I think with Lefors at QB and that biiig RB.