If you have installed the TV Pack onto Vista Media Centre there are a couple of services that wake the pc up one was for the guide update and one was to check if any scedule changes had occured. My HTPC used to do it at 10pm and 3am even although the HTPC didn't have a TV card installed. My main HTPC did it aswell however as it wasn't in the bedroom I never noticed it was waking up every night. Other users reported it doing it at midnight also.
There is no option to disable these updates so I wrote a batch file to stop the services before the PC went to sleep using the MCE standby tool to run the batch file before it put the PC to sleep. More information on thegreenbutton.com if you have installed this pack.
