Dan Marino played in 242 games, while Brett Favre played in 273 games. Here is the average game for each:
Dan Marino: 20.5 of 34.5 for 253.5 yards, 1.7 TDs, 1 INT
Brett Favre: 20.9 of 33.9 for 238.5 yards, 1.7 TDs, 1.1 INT
Other numbers are extremely close, most with a slight advantage to Marino: TD % (Marino 5%, Favre 5%), INT % (Marino 3%, Favre 3.3%), Yards Per Attempt (Marino 7.3, Favre 7.0), QB Rating (Marino 86.4, Favre 85.6). Favre has a better completion percentage (61.6% to 59.4%), but Marino has a better sack rate (3.1% to 4.8%).* Marino's winning percentage as a starter was 61.5%, and Favre's was 62.8%.
The team contexts for Marino and Favre were also similar: both usually had good coaching, usually had good pass protection, both played with often good but rarely great skill position players.
When I consider the careers of Dan Marino and Brett Favre, I see few ways to argue that one or the other was far superior to the other. It's not that you can't make the argument, or find data to suggest one was superior to the other. It's just that their production was so similar, such arguments won't be convincing--they merely reinforce what one was already predisposed to believe.
Oh, but there's that one thing: Favre won a Super Bowl, Marino didn't. For some, that may swing the argument to Favre. But I think that would be blinkered.
These are two QBs that shared remarkably similar careers, QBs that share similar statistics, that share similar winning records. To determine one was better than the other because of one team championship just doesn't make sense.
Marino's best team was the 1984 Dolphins, who went 14-2 and reached the Super Bowl. There they met a juggernaut: the 1984 49ers went 15-1 (their only loss by three points), ranked 2nd in points scored and 1st in points allowed, with a point differential of 15.5 points per game.
Favre's best team was the 1996 Packers, who went 13-3 and won the Super Bowl. The '96 Packers had the league's #1 defense in both points allowed and yards allowed.
So Favre is better than Marino because in his prime he played with a #1 defense? Marino is not as good as Favre because when he reached the Super Bowl his team was beaten by one of the greatest teams of all-time? This doesn't really make logical sense.
Marino and Favre (September 27, 2007)
Some relevant (and great) posts at pro-football-reference.com:
All-Time NFL QBs: The Best Overall QBs Ever
The Best QB of all time?
A last look at QBs
Favre vs. Marino (this is a detailed, researched, analytical, and superb comparison of the two QBs)
*Marino was a gem at avoiding sacks in the pocket--he made slight movements to avoid rushers, instinctively buying time, and also avoiding sacks with his quick release. 10 times Marino had the lowest sack rate in the league, including his first seven seasons.