As of Super Bowl XLVI:
1) Craig Morten - Super Bowls V (Cowboys) and XII (Broncos)
2) Fran Tarkenton - Super Bowls VIII, IX, and XI (Vikings)
3) Roger Staubach - Super Bowls X and XIII (Cowboys)
4) John Elway - Super Bowls XXI, XXII, and XXIV (Broncos)
5) Jim Kelly - Super Bowls XXV, XXVI, XXVII, and XXVIII (Bills)
6) Tom Brady - Super Bowls XLII and XLVI
All of the above were starting quarterbacks. There may be some backups who have also been on more than one losing Super Bowl team.
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Jim Kelly of the Buffalo Bills. He lost four straight (Super Bowls XXV, XXVI, XXVII, and XXVIII).
Fran Tarkenton of the Minnesota Vikings was the losing QB in Super Bowls VIII and IX.
John Elway of the Denver Broncos was the losing QB in Super Bowls XXI and XXII.