Under D:\Console Emulators on my better hard disk! In this folder I have sub divisions for Atari (containing stuff to do with the Atari 2600, 5200 and 7800), Gameboy (includes GB/GBC/GBA), GameCube, Master System, Mega Drive (inc. 32X etc.), NES, Nintendo 64, Playstation and Super NES with an extra folder originally entitled 'Xtras' where I keep all my GoodTools and other rom tools for the various consoles.
In each of these folders contain further folders where each of the emulators are, and of course rom folder(s). For example, my Super NES folder contains a ZSNESW 03.13 folder, a Snes9x 1.42 folder, a rom folder and an 'Advanced Extras' folder that contains misc stuff such as translation documents and my SPC collection.
I have shortcuts to all the emulators I use in my start menu for easy access.