Well, I guess I should have elaborated a bit more, but specifically I'm still using VS2008 so I really don't know if IE9 will affect this or not. I'm assming not, but I've learned to be careful.
EDIT: I guess I should also say that my main concern is that IE can changes system files, and thus this my main concern, as VS2008 has some quirks already with Win 7 64 bit.
Hm, I wouldn't know, I use FF4 and C::B... though I sometimes mess around with VS2010 too. I definitely won't ever launch an IE unless someone forces me, I had some really horrible experiences with it.
I'd guess it probably shouldn't affect anything. In the first place, the actual files IE creates shouldn't be any of those VS cares about.
Oh, I had some issue with VS2008 before when I installed IE8. I messes some of the wizards and GUI of VS2008, so there is a possibility that it would affect programs that render HTML on windows. Some of us might not be aware that .chm files use IE.
It all depends what you're doing. We've seen very strange things happen on boxes with IE8, where even uninstalling it doesn't fix the problems. I'd expect IE9 to be another pack of unknowns.