If you don't want to go for a 'pre-pay rate', but still want to pre-pay, there are hotels that will let you do so, if you send a letter or fax confirming. I've had to do this a couple of times for customers and colleagues (IC Budapest, Meridien Vienna) and had no problems.

If you do go for a pre-pay rate, it depends on the hotel. I've been at some where you definitely get a dodgy room (Hilton Amsterdam springs to mind), and others where a smile gets you an free upgrade (Meridien Vienna - my current favourite hotel...)