I have my monitor turned sideways (fairly common I think). I'd say take the suggestion on how to avoid rotation if at all possible, but otherwise I wouldn't worry too much about it. I actually did de-case mine, which made it easier to mount for me, and it probably wouldn't have fit otherwise - it's a 21" monitor that barely fits depth-wise with the case off.
Since mine is rotated, I specifically wanted a video card that could rotate natively in the windows driver, so I got an ati. I think all their cards support it now (I certainly didn't get a high end one - it was about $45) but you have to run the ati installer rather than just using a bare-bones driver. I'm almost positive that I don't take a performance hit because of rotation (or at least it has been such a non-issue that I'd never guess there's a hit), and as far as windows is concerned, there is nothing out of the ordinary. Literally everything is rotated.
So the comment that Fozzy made regarding the Nvidia drivers certainly isn't true with my ati. The only thing I can figure regarding his comment is if the Nvidia cards come with the Portrait Pivot software, which doesn't work in directx so while I tried it for a while I was never able to really get it to work for mame. As long as a driver supports rotation natively in the driver I think what you want to do should work fine.