Favre's 2007 season ranked as the 103rd best statistical season by a QB, and the 73rd best since the merger. I'll get back to this in a bit on how things look the next year.
Because of Favre's 103rd slot in the rankings, I checked out the top 206 QB seasons of all time. Five of them occurred in 2007 (Brady, Favre, Manning, Romo, Garrard), and five other times the QB did not play the next season. Montana in 1990/1991 (injury), Staubach in 1979/1980 (retirement), Meredeith in '68/'69 (retirement), Van Brocklin in '60/'61 (retirement) and Graham in '55/'56 (retirement). Of the remaining 196 QBs, only three switched teams in the off-season. Of the other 193 QBs (
this is the relevant part of the post), 39 of them played in at least one more game than they started. That's not a perfect proxy for being benched, though. A lot of them (Mike Vick, Chad Pennington, Kurt Warner) had injuries, and came back and played a game before starting, and some old timer's starts numbers aren't perfect. Remove them, and there isn't much left.
Jake Plummer (169th best season in 2005, benched in 2006) is one. I believe Brad Johnson was benched at one point for Jeff George in 2000, so that would be another (Johnson's big time 1999 year ranks just a hair behind Favre's 2007). That's pretty much it, for modern QBs. Even the '80s doesn't give much. Tommy Kramer had a big year in '86, but then stunk and was benched in '87. That's it there. Earl Morrall lost his job in 1969 to Unitas, after winning NFL MVP in 1968. Craig Morton had a very good year in 1970, but lost the job to Staubach in '71.
In conclusion, it would be close to unprecedented if Favre stays on the team and is benched. The best example is probably Earl Morrall, whose 1968 season was, after adjusting for era, just as good as Favre's 2007 year. That's about it, though.