The Wii has an outstanding homebrew scene! I'd go as far as saying it's
the reason to own a Wii.
Seeing as how you already have WiiMednafen, I'd recommend...
Genesis Plus GX
http://code.google.com/p/genplus-gx/This is an enhanced port of Genesis Plus. It's capable of emulating the Genesis / Mega Drive, Sega/Mega CD, Master System, Game Gear & SG-1000 (including all unlicensed or pirate known dumps), also supporting backwards compatibility modes when available.
It is, quite frankly, the most accurate 8-16bit Sega emulator ever written.
Snes9x GX
http://code.google.com/p/snes9x-gx/A Super Nintendo emulator based on Snes9x, ported to the Wii and GameCube. The GUI is powered by libwiigui.
FCE Ultra GX
FCE Ultra GX is an NES emulator based on FCEUX. With it you can play NES games on your Wii/GameCube. The GUI is powered by libwiigui.
RetroArch Wii
http://wiibrew.org/wiki/RetroArch_WiiRetroArch is a modular multi-system emulator system that is designed to be fast, lightweight and portable. This Wii port can run cores for a large number of systems, including CPS1, CPS2, and NEOGEO.
The following emulators/games have been ported to RetroArch and are included in the Wii release of RetroArch:
Final Burn Alpha Cores (CPS1 - CPS2 - NeoGeo) [version 0.2.97.26]
FCEUmm (Nintendo Entertainment System) [recent SVN version]
Gambatte (Game Boy | Super Game Boy | Game Boy Color) [version 0.5.0 WIP]
Genesis Plus GX (Sega SG-1000 | Master System | Game Gear | Genesis/Mega Drive | Sega CD) [version 1.7.0]
SNES9x Next (Super Nintendo/Super Famicom)
VBA Next (Game Boy Advance)
Prboom (for playing Doom 1/Doom 2/Ultimate Doom/Final Doom)
Mednafen PCE Fast (PC Engine/PC Engine CD/Turbografx 16)
Mednafen Wonderswan (WonderSwan/WonderSwan Color/WonderSwan Crystal)
Aside from emulation, I'd recommend installing a CIOS for running Wii games off a USB HDD,
d2x-cios
http://code.google.com/p/d2x-cios/This is a custom IOS for the Wii console, i.e. an IOS modified to add some new features not available in the official IOS.
This custom IOS has been made to be used ONLY with homebrew software.
The d2x cIOS is an enhanced version of the cIOSX rev21 by Waninkoko.
Also a Custom MIOS for running Gamecube games off a USB HDD,
DIOS MIOS
http://code.google.com/p/diosmios/DIOS MIOS (Lite) - Play your Nintendo GameCube games on Wii from an USB device or SD card
and finally a loader for actoully loading the Wii/GC games.
USB Loader GX
http://code.google.com/p/usbloader-gui/This is a program to be loaded on a Wii console. The main purpose of this program is to load Wii games from a USB hard drive, but it includes much more than that.
Make sure you know what your doing first before installing CIOS/DIOS MIOS, since you could brick the Wii if you're stupid about it.