I have only been following FCS for about 8-10 years now but I would say the following.

Montana 1996 (defending national champs and were undefeated until Marshall)
2011 Sam Houston State (undefeated until 17-6 loss to NDSU in title game).
2014 Illinois State (Tre Roberson and Marshawn Coprich were amazing).
2016 NDSU (Numerous wins over top 25 FCS teams and win over #11 Iowa).
2017 James Madison (DESTROYED FBS Eastern Carolina and SDSU and was undefeated headed into national title game. Was also the defending national champs).

Dewey