I applied to two, one of which was an early match at the time, so the hassle and cost practically doubled, above and beyond all the extra interviewing. It's a drag, and it'd be great if you could decide ahead of time which to choose, but if you can't, or if you're using one as a dream and the other as a back-up, suck it up and do it; it's certainly possible to accomplish and you'll kick yourself later if you blow it (e.g., not following your dream or not having a back-up and not matching).
I didn't have any double-interviews-at-the-same-hospital problems, but actually, an applicant I met on an ENT interview spotted me at UCSF during my anesthesiology interview there (she was doing her anesthesiology rotation). I had no idea (apparently she sat right across from me at lunch), but she later matched with a good friend of mine, who relayed the story to me. It's a concern, though, and it's probably best to try to avoid applying to both types of programs at the same hospitals, or at least have a really good story for why you're doing it.
