Here is my personal list.Im hoping it can help some of the newer emulation enthusiasts in choosing their emulators.I do take compatibility over features in choosing the emu's I use.
System Emulator
Atari 2600 Stella
Atari 5200 Kat5200
Atari 7800 Prosystem
Colecovision MESS
Mattel INTV Nostalgia
Arcadia 2001 MESS
Sega SG1000 Fusion
Famicom Nestopia
Nintendo FDS Nestopia
Nintendo NES Nestopia
Sega Master Fusion
TurboGrafx16 Mednafen
TurboGrafx16CD Mednafen
Sega Genesis Fusion
Sega CD Fusion
Super Nintendo bsnes v.88
Super Famicom bsnes v.88
3DO 4DO
Sega 32X Fusion
Jaguar Virtual Jaguar
Satellaview Snes9x
Nintendo 64 pj64 1.6.1
Sega Saturn SSF
Sony PSX Mednafen WIP
Dreamcast NullDC
Playstation 2 PCSX2 v1.0
Nintendo GCN Dolphin
Nintendo Wii Dolphin
Vectrex ParaJVE
Adventurevision MESS
Atari Lynx Mednafen
Gameboy Gambatte
Gameboy Color Gambatte
Gameboy ADV VBA-M
Game Gear Fusion
Virtual Boy Mednafen WIP
Nintendo DS Desmume
PSP JCSP
Pong DICE
Naomi Demul
Atomiswave Demul
