As scenarios go, it was a 3-point game, any number of things could've changed the outcome. Even just a modestly better defensive performance would lead to an Eagles victory, so a healthy TO would've been able to switch it up. Even just assume he makes some dynamite play in the last few minutes.
It changes the dynamic of things in Philly obviously; the championship drought ends 4 years earlier than OTL (when the Phillies won in 2008) and may actually reduce the bandwagon effect when the Phils get hot in 2007-2010.
The fundamentals of the Eagles don't change much at first, they still have the basic issues with Owens and he probably still leaves, and things play out more or less as they did IOTL through 2009. But I don't think that Donovan McNabb gets traded to the Redskins, and he may have enough halo effect to continue to play for the Eagles into 2010, missing the playoffs and derailing the whole Vick era. After 2010, the team goes through a proper rebuilding effort instead of the "Dream Team" win-now moves. Hey, we can hope.
If he plays otherwise the same but wins SB XXXIX, McNabb is probably an actual HoF contender. Especially as the second black QB to win a Super Bowl.
Tom Brady wouldn't be as highly regarded as IOTL - since he would have won two instead of three Super Bowls - but I can't imagine him or Belichick ever going on anything but their own terms in New England.