Using the Homebrew Disc Channel, you can load homebrew programs from regular ISO9660 DVDs. It supports (sub)directories.

Note: The name Homebrew Disc Channel is actually wrong; the program was intended as either an add-on to the Wii Disc Channel or a separate channel, but due to the fact that BootMii will need a SD card to load, turning this program into anything other than a regular homebrew program will be useless in a couple of months.