It would depend on how Democrats use their majorities in Congress vis-a-vis President Bush. If, like the Republicans of 1994 (assuming Democrats gain control of both houses of Congress by similarly lopsided margins this November), they overreach themselves in pandering to the extreme Bush-hating elements of the party, we could see a possible Republican resurgence in 2008, which could also affect the presidential race.
That's true; the chances of the Republicans winning the Presidency in 2008 would probably be increased if the Democrats take control of Congress this year.
Which is why I think Democrats would be better off to gain seats in both houses of Congress this year, while leaving Republicans with enough of a majority that they would be blamed for whatever happens as the party in power, but not enough to overcome Democratic opposition to whichever policies they choose to pursue. This would be the worst possible outcome that would befall Republicans this November. They will get very little -if anything- done, but they will get all the blame for the war, rising deficits and debt levels, inaction on global warming, as well as being stuck with an increasingly unpopular president, all of which could combine to give us a perfect storm that would enable us to take control of not only Congress, but also the presidency in 2008 (assuming we nominate Mark Warner).