SMYGB 0.20 - Windows - SMYGB is an EXCELLENT GameBoy emu, emulating regular, Super and Color versions of this handheld. The sound in SMYGB is truly magnificent, the compatibility is awesome!
Dboy 0.55a - DOS - DBOY came out of nowhere and has established itself as one of the BEST GameBoy emus out there. Dboy emulates all 3 versions of the GameBoy and it is also updated every few days, adding new things and fixing bugs. This is one to watch out for!
Gameboy 98 0.05c - Windows - Gameboy 98 is a nice Gameboy emu with lots of options and DirectX support. Color Gameboy is also emulated now.
No $$ Gameboy 2.3a - DOS - NO$GMB (No cash Gameboy = free ;) is an awesome emualtor. It can emulate upto 12 gameboys at a time, it runs full speed on a 386/33 and above and it emulates Color and Super Gameboy too! 100% ASM rocks !!
GB FAN Plus 1.15 (6th) - Windows - GBFAN is a Japanese Gameboy emu and it's pretty fast. It's for WIN95/98 and uses DirectX. Not much is known about it, since it's ALL in Japanese :)
HelloGB 03.09 - Windows - HelloGB is a new Gameboy emulator, which emulates Super and Color Gameboy. This REQUIRES DirectX 5.2 or higher, so it will NOT work in NT. If you're having trouble running it, try using the "/nodsound" switch.
REW 0.9LC - Windows - REW is an Gameboy emulator by the author of Dboy, it also supports some NES mappers.