Unzipping or copying a file to Program Files in Vista/Win7 I can see would cause a problem, but that's because those OS have it protected like you said. If you copy or extract a program, let's say a game into C:\Games\GameName, then it has the permissions of the person who made the folder and should work.
You don't need to go quite as far as making a whole separate partition to get this to work, just making a \Games\ folder or something on your hard drive that is not in \Program Files\ should work.
I don't really see the point in having a separate partition to install things to if you're not planning on reinstalling it in the future when you reload your OS. If you have data you're storing, like MP3s, documents, pictures, videos, then it makes sense. But why install apps on another partition if they'll just need to be reinstalled anyway? Might as well put them on the main partition in another folder.
That makes me wonder a little is this: I copied a game from one PC to another, even a different version of Windows to another, and it works without any problems. A large game, Aion, if anyone's familiar with it. I'm sure it had registry entries, dlls, and anything else that normal installers would have placed. But even so, after copying it from a WinXP 32 bit machine over to a Win 7 64 bit machine, it runs flawlessly.
So my point is why have all the registry entries, dlls, and stuff like that if they aren't needed? Is it because each program would then be huge, like Johngalt suggested? Aion is huge. Almost 7gb I think.
What I'm more interested in though is I'm sure it made registry files and had dll shares and things like that going on but apparently it doesn't need them to function. I wonder how many other programs are like that? Why make the entries at all if they end up not being needed? Simply for file associations, and so the program can be cleanly uninstalled?
However! Would it need to be cleanly uninstalled if it wasn't installed with an installer in the first place?