My ranking of all-time is pretty much the same group as everyone else. Really there are two (2) categories as I see it.
Top wins vs best opponents (who was the best team we defeated, despite rankings):
1. 1990 vs Miami
2. 2018 vs Wisconsin
3. 1980 Miracle Bowl vs. SMU
4. 1997 Cotton Bowl vs Kansas St.
5. 2009 vs Oklahoma
Realistically, it's hard to say which teams we beat were the best teams as there are a lot that could be in the debate for #5 (see link to article at end of this post)
Top 5 best wins (this has no direct correlation on whether the opponent was as good as touted, but the wins had the greatest effect on the BYU football program:
1. 1984 vs. Pittsburgh (It didn't end up mattering that Pitt didn't turn out to be worthy of a #3 ranking. The win acted upon us as though they were and directly affected our run to the national championship.
2. 1984 vs. Michigan (we don't win, we have no claim to a national championship)
3. 1990 vs. Miami (set Ty Detmer up for his Heisman run)
4. 1980 vs. SMU (Miracle Bowl and BYU's first bowl win)
5. 1979 vs. Texas A&M (1st signature win for LaVell Edwards on a national scope)
Once again, beginning at #5, there are so many games that could be argued as in that range. In an article in July 2016 for KSL, Mitch Harper gave his opinion on the top 50.
https://www.ksl.com/?sid=40661381&nid=272