This here is a simple list of tools available on the interwebs for Pokemon hacking/modding. 

Disclaimer: I don't own these. Any of these. I didn't make these tools.

Generation 1Edit

Swampert Tools - The best out there. It's a compilation of tools used for editing Red, Blue, and Yellow. I'm not sure if it works on the Japanese Green version.

Generation 2Edit

Nothing that I can recall! There are some out there, I'm sure of it!

Generation 3Edit

Advance Map - A very handy tool that is used for mapping. Want to make a completely new game? Or just add a new dungeon? This is what you need. It can also edit wild Pokemon that spawn, trainer sprites, and scripted events (provided you link it with a script editor.). 

Advance Text (A-Text) - Advance Text is a tool that sounds pretty simple, but it can get very technical when you push boundaries. It is used for editing phrases and lines said throughout the game. You could even change "Fainted!" to "Died!" if you wanted to. It comes preset with drop-down menus for the beginning segments of the game, but comes with a search function that allows you to find and edit specfic pieces of text in the game.

DNS - DNS is a remarkable tool used for implementing a day and night system into the games. It also allows you to insert a seasonal system as well, which you can customize the exact months of to your liking. 

Lunar IPS - This tool is useless unless you actually make a hack or mod, okay? But this is how you get it out there! It creates an .IPS patch of your modded ROM file, allowing you to upload it. IPS files are perfectly legal, by the way. Of course, it also allows you to patch a clean ROM with an IPS file.

Nameless Sprite Editor (NSE) - NSE is meant for editing sprites. It's a bit like MS Paint, but is much better! You can edit every little pixel with this cool program. 

Advanced Series - Advanced Series is a great sprite editing tool as well, but is meant for Pokemon sprites rather than trainer sprites. You may find sprite projects on the web that assist you in using this tool better. Wichu's Sprite Editor can be used a lot faster if you have sprite "strips" of the Pokemon's front, back, shiny front and shiny back sprites. These can be easily imported into the game. They then can be repositioned with the Sprite Position Editor in Advanced Series.

X-Treme Script Editor (XSE) - Wanna get really into ROM hacking? If yes is your answer, you'll have to be scripting at some point, unless someone is doing it for you. Although you should learn. It's very worth your time. With scripting, people have managed to put stuff like the new Fairy type in FireRed, and create new events entirely.

Free Space Finder (FSF) - Free Space Finder is a simple little tool that can search for free script blocks in the game data and give them to you, so it's easier to repoint things when using another tool. Although, tools like the ones in Advanced Series have built-in FSFs. 

Gen 3 ROM Hacking Suite - Here's the big one! This can edit sprite data without Advanced Series, can support more than 17 types, edit Pokemon's stats and moves, and even expand the Pokedex in FireRed! Allowing for all 719 Pokemon to be put in the game! Here's the downside: As of now, ROMs that are used by the hacking suite can not be used in Advance Map. Due to that, the only way of putting all these new Pokemon in the game is a script editor.

Generation 4Edit

PokeNav - This isn't really a mod tool. It just lets you get any Pokemon you want in your box. Works for Gen 5 too.

Generation 5Edit

PWT Editor - Were the tournaments in BW2 too boring for you? Fix it with this tool!