And at the same time, how should they be kept separate for multiple users?
...
Of course, there's no real reason why mIRC has to use AppData for those things (or even for settings). It could just use Documents and Settings and place the files within the user's folder there. I'm not sure if that folder is in Vista, but it probably is.
You just answered your own question. Which is what the OP was saying too. Put the downloads folder in a subdirectory of the user folder, just not the AppData folder since it's hidden.