This is second take at this thread. Hopefully, it will be more up-to-date. I've updated the links and added a lot of new tools (some were just random searches on Google, some were took from the old thread). If you have any suggestions, feel free to mention them.
Nintendo Entertainment System (NES)
- Adventures of Lolo 3: Level Editor
- Arkanoid: ArkEdit (DOS) - Alkalavista (Mac OS X)
- Battle City: Quarel
- Castlevania: Stake
- Final Fantasy: FF Windows - FF Hackster Companion - FF Hackester - Final Fantasy 1 Improvement (DOS)
- Gimmick!: Level editor
- Kid Icarus: Pit Stop
- Kirby's Adventure: DreamTool
- Legend of Zelda: Dungeon Master - Zelda Tech
- Moai-Kun: Moai-Senpai
- Mega Man: Rock and Roll
- Mega Man 2: Rockman 2 Editor (apparently it works with Mega Man 2)
- Mega Man 3: Rockman 3 Editor (works with Mega Man 3 too)
- Mega Man 4: Rockman 4 Editor (works with Mega Man 4 too)
- Mega Man 5: Rockman 5 Editor (works with Mega Man 5 too)
- Rockman 6: Rockman 6 Editor (this will NOT work with Mega Man 6)
- Metroid: Editroid
- Tecmo Super Bowl: Tecmo Super Bowl Manager
- RBI Baseball: RBI Editor (in-browser)
- Super Mario Bros.: Insectduel's SMB Utility - SMB Utility - SMB ROM Text Editor - SMB Fix - YY-MarioEditor - SMB Graphics Workshop - Mario's Beauty Salon
- Super Mario Bros. 2: SMB2 Discombobulator - SMB2 Transmogrificator
- Super Mario Bros. 3: Reuben (useless, look below) - Mario Improvement 3 - SMB3 Discombobulator - Map Editor - Vegas - SMB3 Workshop
Nintendo GameBoy (GB)
- Mega Man: Dr. Wily’s Revenge: Wily's Toolbox
- Pokémon: Pokécommunity (board) - Tools (external forum) - Also some tools (external forum) - G2Map
- Super Mario Bros. Deluxe: Super Mario Bros. Relocaverburator
- Super Mario Land 2/3: MooJelly
- Zelda: Oracle of Ages: ZOLE
Super Nintendo Entertainment System (SNES)
- Angelique: Angelique Tile Editor
- Bust-A-Move: Shampoo
- Chrono Trigger: Shop Keeper - Item Name Editor - Crone - CTENED - Gears - Temporal Flux
- Clock Tower: Text Edit
- Donkey Kong Country: Donkey Kong Country Resource Editor
- Earthbound: EarthBound Map Editor - EarthBound Sprite Editor - EarthBound Store Editor - PK Hack - Don't Care Editor and EB Text Compressor
- Final Fantasy 2/4: ff4h SRAM Hacker - FF4kster
- Final Fantasy 3: Sprite Editor - Multi Editor - Shop Editor - Sprite Editor - Weapon Tool - US Editor Hack - Mac Thing
- Final Fantasy 3/6: ff3h SRAM Hacker
- Final Fantasy 5 (J): Multi Editor
- F-Zero: Fuzee
- Harvest Moon: HME - HME Dialogue Editor
- Mega Man X: MegaED X
- Mega Man X2: MegaED X
- NHL '94: NHL '94 Editor
- Panic in Nakayoshi World: NaCHAOshi
- Sailor Moon RPG: Map Editor
- Super Mario Kart: Track Designer - Epic Edit - MAKE - mKedit
- Super Mario World: Tools link on this website
- Super Metroid: SMILE
- Tecmo Super Bowl 3: Manager
- Tetris Attack: Block Edit
- Zelda - A Link to the Past: zcompress - Zelda Script Editor - Hyrule Magic
- Top Gear 2: TG2Edit
Sega Genesis (GEN)
- NHL (General): NOSE
- Sonic (General): Sonic Retro (board) - Sonic Hacking Utilities
- Sonic the Hedgehog: SonED - Esrael Sonic Editor
- Sonic the Hedgehog 2: Esrael Sonic Editor 2
- StH 1 / StH 2 / StH 3 / S&K / Sonic Crackers: SonMapEd
Nintendo 64 (N64)
- GENERIC: LemASM
- Banjo Kazooie: Text Editor - Banjo Kazooie N&B Vehicle Editor
- GoldenEye: 007 Face Mapper - ROM Editor
- F-Zero X: Execution Project
- Perfect Dark: Face Mapper
- Super Mario 64: Jul (board) - Toad's Tool 64 - Mario 64 Level Importer - mml2m64 - MusicXML - M64 ROM Extender - M64Tool
- Zelda: OoT / MM: z64porter (rest is down)
Gameboy Advance (GBA)
- Final Fantasy IV: FFIV Advance Editor
- F-Zero Climax: Course Editor
- Mario & Luigi: Superstar Saga: Yoshi Magic
- Metroid Fusion / Metroid Zero Mission: DoubleHelix
- Pokémon (General): Pokécommunity (board) - Tools (external forum) - Some RSE tools - Elite Map - Advance Text / OverworldEditor - Rebirth Edition - iconED - PokemonAmp - Advance Attack - Advance Mart - Advance Starter - IntroED
Nintendo Gamecube
- Legend of Zelda: Four Swords Adventures: EFSAdvent
Nintendo DS (NDS)
- Mario Kart DS: Mario Kart Course Modifier (requires Autodesk Maya 5, 6, or 7, which isn't free software) - Tutorial
- New Super Mario Brothers: The NSMB Hacking Domain (board) - NSMBe
- Pokémon Black & White: Pokécommunity (board) - Some tools
- Super Mario 64 DS: SM64DS Editor
Nintendo Wii (Wii)
Note that those tools weren't tested, so they might not work. Reuben needs certain ROM with everything moved around to work correctly, and it's not part of the editor - normal SMB3 ROM doesn't work. The IPS of it would include whole game (except for levels). Just use Google to search it because SMWC doesn't allow ROMs... Too bad...