you can store those elf files on your hdd or a usb flash drive using ulaunchelf.
pgen works fine from the hdd and flash drive, snes-station you need to get the unofficial 0.24 to play roms off of the hdd and flash drive. you can do a lot of things having a hdd in your ps2. also SMS can read your audio/video files off of a hdd so you don't really need optical discs