My major concern really in giving the Democrats an easily-available filibuster-proof majority is...well...
Quite simply, although the Democrats being able to defeat attempts by the Republicans to block bills is good, it may be completely cancelled out by the fact that it now makes (well, will make, once they seat Franken) Joe a very powerful man, because he can stop any bill that the Republicans unite against from getting through a filibuster.
Now, this isn't as bad as it may sound, of course; with the Maine Republicans still around, his support won't always be needed, and the Democrats aren't going to always be united either. Yet, there is potential for a good few votes to end up in his hands; the difference between 57-41-1-1, and 58-40-1-1, as I see it, is that the filibuster breaker is too tangible. The Democrats will now KNOW they can get it without Republican support, and they'll be more inclined to pursue the agreement of Lieberman in order to secure a solid 60-seat majority on bills. This gives him power, power that is probably undue and is borne out of perception rather than his real influence, but power nonetheless.
I may be overreacting slightly, however. Yet, I still don't think Specter's defection is really as good as it's being made out. They don't even have the benefit of a lot of publicity on account of the hideously poor (from a partisan standpoint) timing.