Not sure how but I had this problem but don't know. I installed a third-party HD audio driver for Vista Beta dated circa this summer, I then uninstalled that and installed the old XP driver (which, not surprisingly, didn't work) based on a suggestion I found in another newsgroup. I then deleted that driver and let Vista re-install its native HD audio driver. Sound now works with Skype and other apps.
I know this makes no obvious sense but thought that I should pass it on in case it could do the same for others. Vista developers might be able to figure out from this sequence what might be happening. There is a problem here.