Besides Nintendo's Virtual Console (obviously), which are emulators covering:
- MSX, NES, some Arcade boards, SNES (minus games with extension chips), N64 (minus any extensions), for the Wii / Wii U
- Some of the above plus GameGear and Gameboy (Color) for the 3DS
- Some of the above plus GBA and DS for the Wii U
(Keep in mind that GBA VC on the 3DS is actually running on native firmware, much like PS1 Classics on the PSP.)
Nintendo at least developed:
- A Nintendo DS partial emulator for PC (the leaked EnSata)
- A Gameboy Advance emulator for the GameCube (used in an obscure Naruto compilation by Tomy, and a Pokémon GC game, low/medium compatibility)
- A N64, plus NES emulators for the Gamecube (used in the Zelda compilation)
- A NES emulator for the Gameboy Advance (used in the Famicom Classics)
Sakurai said Kid Icarus was first tested on PC and Wii, so... maybe one for the Wii on PC? (because PowerPc architecture is very different from x86, and reprogramming from scratch would be a waste)
Konami developed:
- A NES emulator for PC (they re-released three NES games on PC, with the Nintendo logo removed)
SNK developed a Neo-Geo emulator for their Metal Slug compilations, for PC, PS2, PSP, Wii...
They, along with other developers, also emulated Arcade images for their various re-releases.
Sony developed:
- A PSP emulator for PC (spotted during an E3 show)
- A PS1 "emulator" for the PSP (I don't like this name)
- A PS1 emulator for the PS3 (PSN Classics)
- A PS2 emulator for the PS3 (PSN Classics)
Sega pretty much developed Master System/GameGear/Genesis emulators (minus the Sega CD -laziness- and the X32 -technical issues- and of corse no Saturn -Tengai Makyou IV/Princess Crown PSP were *ports*-) for the PC, DC, PS2, GC, Wii, PS3, XB, XB360, DS, PSP, 3DS, iOS (I'm not talking about the rebuilt engines) and everything that has those Sonic compilations.
Whenever they develop stuff, it's safe to assume they run the test build usually on the console itself and not on PC (the risk is simply too high to include a PC emulator , should a leak happen -and it certainly will-).
That's why dev kits include debug consoles. AND the test build format itself is incompatible with the retail consoles, sometimes fundamentally.