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Basically if a program tries to modify anything in C:\Program Files\ then Vista if UAC is active will redirect it to another per user directory. It does this for certain registry keys as well like HKLM.

And it doesn't just Do The Right Thing if you turn off UAC?

Well. If UAC is on then your request for C:\Program Files\SuperApp\Config.ini goes to something like C:\Users\tfabris\appdata\SuperApp\config.ini. If you've installed your app with UAC on and then turn UAC off at a later point then stuff will have "vanished" until you turn UAC back on. You don't get any fine grain control about what parts of UAC you're turning off. Its everything or nothing.