This is my own personal ranking of the FCS National Championship teams since 2000. 2000 is kind of an arbitrary cutoff because I don't want to make the list too long and I want to go with teams I have watched.

1. NDSU 2013 - not sure I'm convinced they are the best ever, but definitely the best since 2000. One of the best FCS/IAA defenses ever and an offense probably in the top 10 or 15 all time as well.
2. App State 2006 - late in the season after Armanti Edwards got the hang of things, this was a very formidable team. Lot's of talent on defense and lots of team speed. Great coaching staff, too.
3. NDSU 2012 - NDSU 2011 with more overall experience
4. App State 2007 - A very good offense…an underrated defense that faced a lot of offensive firepower both in the SoCon and the playoffs.
5. NDSU 2011 - Outstanding defense, offense is pretty good but not great
6. Delaware 2003 - A lot of people put them in one of the top 3 or 4 all time…I'm not convinced the playoff field was all that great that year. I think that Colgate team is one of the worst teams I've seen in a NC (no offense).
7. NDSU 2015 - When this team caught is stride late season with Carson Wentz back no one was beating them
8. Eastern Washington 2010 - solid on both sides of the ball…downed quality Delaware and NDSU teams in back to back games to take the title
9. App State 2005 - very good defensively, good on offense, won the NC in what is IMO the strongest playoff bracket since 2000
10. JMU 2004 - a team that grew up late and played in a tough CAA…won every playoff game away from home
11. Richmond 2008 - very good on defense, though I do think they lucked out with Armanti Edwards recovering from a hip pointer. Nice combo of Eric Ward and Tim Hightower on offense.
12. Montana 2001 - Glad we caught Montana the year before
13. Georgia Southern 2000 - rebuilding on offense, good on defense. Beat two teams they probably shouldn't have beat in Delaware and Montana.
14. NDSU 2014 - the weakest of the NDSU title teams
15. Villanova 2009 - A team that didn't dominate but just found a way to get the job done.
16. WKU 2002 - I might bitter from the semifinal game that year, but I just never thought this team was that overly dominant

Criticize away.