At one point I used to use Hotwire and Priceline Name Your Own Price... the upside was that (back when I used to use them for car rentals, at least) they offered a pretty good rate and convenience in that you didn't have to shop around. While there may be other downsides, the biggest one for me is inability to cancel for free. Once you buy on HW/Priceline Name Your Own Price, you're locked in. In my experience, I find that prices sometimes come down or plans change, so I like having the flexibility to cancel and rebook as needed.

In every other respect though, using HW/PL is indistinguishable from any other method. They treat you the same at the desk so far as I can tell, and if anything I probably got upgraded most often on HW/PL reservations although I'm sure that was just a coincidence.