Here's where I stand now; almost every system I have has been modified or tinkered with in some fashion, most by me.
Consoles
Atari 2600 Heavy Sixer (S-video mod)
Atari 2600 Jr. (AV mod)
Atari 5200 (S-video and power jack mods)
Atari 7800 (S-video)
AV Famicom
ColecoVision (component video)
Dreamcast
Famicom (AV modded)
GameCube + Game Boy Player (Indigo)
Japanese Sega Master System (S-video)
Japanese Sega Mega Drive (English/Japanese switch, stereo audio jacks)
N64 (RGB)
Neo Geo AES (S-video, Unibios)
NES front loader (external audio mod)
NES top loader (AV)
PC Engine (S-video)
PC Engine Duo-R (RGB, S-video, AV jacks, region switch)
PSX (modchipped)
PS2 (fat, modchipped with internal hard drive)
Sega Genesis 2 (S-video, region switches, Crystal Clear Audio Mod)
Sega Mark III (amplified RGB)
Sega Master System (FM audio, region switch, BIOS mod)
Sega Mega CD II
Sega Saturn (model 2)
Sega SG-1000 II (AV)
SNES mini (RGB and S-video)
Super Famicom (AV jacks, region and lockout switches)
Computers
Amiga 500 (internal 50/60 Hz jumper)
Atari 800 (S-video)
Atari XEGS (S-video)
Commodore 64 (S-video)
Commodore VIC-20 (S-video)
Sony HB-F1XDJ (MSX2+ system, modded with S-video and 256K RAM)
Handhelds
Game Boy (gray, backlit)
Game Boy Advance (white)
Game Boy Advance SP (black, backlit model)
Game Boy Color (purple)
Game Boy Pocket (silver)
Game Gear
Sega Nomad (English/Japanese region switch)
TurboExpress (switchless region mod)