Finally got around to doing this after mentioning it back in January.
https://docs.google.com/spreadsheets/d/1FAdlm8B9ZCxuDPL6nu0Q63yW_qn9Cp-J...
Essentially:
I. College Football Playoff years (2014-2016)
* Automatic Qualifiers (AQ) from the champions of each of the following, regardless of ranking:
-ACC, Big Ten, Big XII, Pac 12, SEC
-The highest ranking Group of Five Champion
* Two (2) at-large selections based on college football playoff ranking. Notre Dame will always eat one of these at-large selections if they're one of the two highest ranked non-AQ teams
* In the case that an AQ team is ranked 21st or lower in the final College Football Playoff rankings, then a second bracket is created replacing each such team ranked below 20th with additional at-large teams until all eight teams are selected.
II. Bowl Championship Series years (1998-2015)
* Automatic Qualifiers (AQ) from the champions of each of the following, regardless of ranking:
-ACC, Big East (when it existed), Big Ten, Big XII, Pac 10/Pac 12, SEC
-The highest ranking non-AQ champion OR Notre Dame if they're ranked higher than all non-AQ champions and in the top-15 of the final BCS standings, or of the last AP after Championship Weekend in years the BCS only ranked the top-15 teams
* One (1) at-large selection based on BCS ranking.
* In the case that an AQ team is ranked 21st or lower in the final BCS rankings (or the AP poll in years that the BCS only ranked the top-15 teams), a second bracket is created replacing each such team ranked below 20th with additional at-large teams until all eight teams are selected.
Of note, the following years have two brackets, with the following teams ranked below 20th:
1999-2000: Stanford
2004-2005: Pittsburgh
2005-2006: Florida State
2010-2011: Connecticut
2011-2012: West Virginia
2012-2013: Louisville and Wisconsin
Don't have time right now, but if people want to see what a 16-team playoff bracket for those years using the champion of every conference + at-large teams would look like, let me know. My personal opinion? If the season weren't already as long as it is I'd say a 16-team playoff will give a better/truer playoff, but without compromising the 12-game schedule + Championship Week, 8 is enough for now.
EDIT: Just added an appearances by team tab. Any team that lists "X or Y" is either benefiting from a different team not being ranked in the top-20 (like California) OR have an appearance where they aren't ranked in the top-20 (like FSU in 2006)

Comments
I was a little confused by the times you said "highest non-AQ Champion," until I realized you meant "highest AQ non-Champion."
Still, though, good work.
I think he meant it the first way. Champion of a conference that doesn't have AQ status. The BCS equivalent of G5.
I know what a non-AQ champ is, but his sheets where he replaces an AQ champ with another team don't jibe with the phrasing "non-AQ champ."
Three examples:
1998 - replaces Pac-10 champ Stanford with Big 12 non-champ Kansas State
2004 - replaces Big East champ Stanford with Pac-10 non-champ California (MWC champ Utah is in both tables)
2005 - replaces ACC champ Florida State with Pac-10 non-champ Oregon (MAC champ Marshall is in both tables)
Ah, I see what you're getting at. Hyphen not carrying far enough.
Got it. Like em-PHA-sis on the wrong syl-LAB-le.
16 team playoff, every FBS conference champ gets a bid. 5 at larges. Let's go.
yeah, but exams or whatever the excuse is that lets fcs schools do it and not fbs!
Ew no. I don't want to see Bama basically get a bye each year when they play some crappy MAC champion.
I figured it would be the lowest ranked conference by some metric, conceivably always the Sun Belt.
I'd have at-larges seeded 12-16, just like NFL wildcards.
No way, that would mean that the 6 seed would actually have the easiest matchup playing the MAC, Sun Belt, C-USA champ.
The 6 seed would also most likely be a G5 champ, so most years you end up splitting hairs as to which G5 conference has the strongest champ.
What on earth happened in 2009-10? I must have wiped that from my memory but if the CFP was in place and Cincinnati and TCU made it that would be bizarro world.