Being brand new to multi-boxing (I'm tripling Mages) WoW (I played Alliance on Magtheridon with Xzin and his clones, so he's the one that inspired me to do it), I've picked up a few ideas from him, these forums, and my own experiences.

I would not unbind WASD on the clones. Do as the others have suggested and set WASD to the "Do Not Pass" list. I bound the arrows to move all, but they get used very, very rarely.

F9-F12 are keybound to do the following:
F9 moves the clones forward without moving main window.
F10 moves the clones backward.
F11 moves one clone left and the other right.
F12 move the first clone right and the other left.

The F11 and 12 bindings seem weird, but I've found it useful for ensuring LoS in some places.