Yeah, as I was typing my last reply the same thought occured to me. I think it was Chase who once said something like:
"They're just too nasty to each other not have been... nasty"
And this was towards the end of the season one episodes, with Vogler the big Pharamceutical dude who was chairman and tried to oust House from the hospital.
I suspect the next episode, if not next season, might have some clues about what exactly happened between Cuddy and House back when they were at uni...