I love the concept of emulators being triggered by file extensions. Thus I can just pick my preferred versions of multi-platform games, have them all in ONE place and can select them using ONE interface, without having to launch a specific emulator first. Simple idea, but it rocks!
So, on the whole, while I have complete system libraries on my SD card, the "GAME" folder serves as a cross-platform pool just for favourites. I like it.