WiiWare/VC launched through the SD channel? I haven't seen anything yet homebrew wise. The only way I know is to manually put them in the order desired like you mentioned.
I am looking for a tool, or app, that will organize games that are on the sd card. I am aware that I can move the channels myself. I was wondering if there is one that you can just hit a button and alphabetize, or perhaps a most played button.