Silence Cave from "Lagoon" (SNES)
Castlevania - Ballad Of Angels
Castlevania - The Castlevania Dungeon
Castlevania - The Inverted Castlevania Dungeon
Ecco The Dolphin - Caverns Of Hope
Final Fantasy - Endless Nova
Indiana Jones And The Fate Of Atlantis II
Kaboom! - Kaboom Online
Katamari Damacy
Lagoon - The Lagoon Shrine
The Legend Of Zelda - The Legends Of Zelda
The Legend Of Zelda - The Obelisk Of Hyrule
The Legend Of Zelda - The Ocarina Of Time 2D
Lunar - LunarNET
Mega Man - The Mega Man Home Page
Metroid - The Metroid Database
Metroid - Project Ridien
Pac-Man - The Pac-Page
Phantasy Star - Algol Star System
Phantasy Star - The Phantasy Star Cave
Phantasy Star - The Phantasy Star Pages
Phantasy Star III - The Complete Guide To Phantasy Star III
Secret Of Mana - The Secret Of Mana Theater
Shining - Shining Force Central - Uniting The Powers Of Light Online!
Snood
Sonic The Hedgehog - The Green Hill Zone
Sonic The Hedgehog - Secrets Of Sonic Team
Sonic The Hedgehog - Sonic Cult
Sonic The Hedgehog - Sonic Fan Games HQ
Sonic The Hedgehog - Sonic Strike
Spyro The Dragon
Super Mario Bros. - Mario Fan Games Galaxy
Super Mario Bros. - The Mushroom Kingdom
Super Mario Bros. - SMBHQ
Super Mario Bros. - Super Mario 128 Central
Super Mario Bros. - Super Mario Portal
Super Mario Bros. 2 In 3D
Some of the emulation sites below are very pop-up heavy, so downloading and installing Google Toolbar might be a good idea.
Aeon Genesis Translations
AtariAge - "Have you played Atari today?"
AtariGuide - "The Atari Collector's Resource"
Cherry Roms - SNES ROM Heaven!
China GBA - GameBoy Advance ROMs!
DeJap Translations
Edge Emulation - almost all the ROMs and ISOs you could ever hope to have, although ISO access comes only at the cost of $30, which helps pay for bandwidth
Eidolon's Inn
Eight Bits Of Joy - NES ROM Heaven!
EmuAsylum
EmuParadise
EmuVortex - GameBoy Advance ROMs!
Fantasy Anime RPGs
Gens - a nice Sega Genesis, Sega 32X, and Sega CD emulator
MAME - Multiple Arcade Machine Emulator
MAME World
The N64 Emulation Support Centre
N64 ROMs
RetroBase
RPGd Translations
Snakeyes Gaming Corporation Translations
The Whirlpool Translations
Zophar
ZSNES - a nice Super Nintendo emulator
Castle Paradox
Flying Omelette
GameFaqs
I-Mockery
Lost Levels
Metroid Metal
OverClocked ReMix - Unnofficial Game Music Arrangement Community
SegaFans
The Video Game Museum
Video Game Music - MIDI Heaven!
Atari
Blazefire Productions
Gregorsoft
Kemco
Konami
Namco
Neave Games - classic arcade games resurrected by Flash software
Nintendo
Sega - Sega!
Square Enix
Treasure Games, maker of "Dynamite Headdy" and "Gunstar Heroes"
Working Designs