Same size as a GBA game, so it will stick out about 1cm. If you don't want any sticking out, get the M3 Lite (uses microSD) not sure if/when it's out though.
Along the lines of the MiniSD M3, I can't seem to get any homebrews to work with it. I tried out dsDoom and Hexen, and neither one works for me. I am doing the correct process with the correct .wad files, but Hexen doesn't run and dsDoom gives me black screens with a message like "graphic something or other failed". Please let me know if I am destined not to have homebrews on my MiniSD M3... I have heard it works on the CF and the regular SD, but not the MiniSD. I am not talking about the new MicroSD, just to clear that up too. I didn't want to start a new thread either, because I thought it could be answered in this thread. Sorry if I am mistaken.