when it comes to software i add of course the Homebrew Browser, USB Loader, i forgot what it was called but the thing that allows you to install WiiWare and Virtual console games, then dedicated emulators for NES, SNES, GB/C, GBA, Master System, GameGear, Genesis and PCEngine would do more emulators if i knew they worked well.
hardware modding would probably be the HDMI video mod and i can't really think of anything besides that