First of all, you should know that hacking Pokemon games are illegal, or at best in a legal grey area. Now that you know, proceed at your own risk. There are some Pokemon games that everyone wanted to exist at some point. Hacking tools exist to make it easy (or at least easier) for the average computer literate person to hack Pokemon games.
The first step is to select your ROM. This is the game itself. The hacking tools vary for each generation. Pokemon Red and Blue (Gameboy Color) will have different hacking tools than Pokemon Ruby and Sapphire (Gameboy Advance).

'-----------------------Simple text editing is as good a place to start as any for the novice hacker. Advance Text for the third generation is very noob-friendly. It is an easier alternative to those who do not understand scripting. If you think you can ace scripting on the first try, here's what it looks like:

#org 0x165D9A
lockall
setvar 0x4001 0x1
goto 0x8165DBE
end
'-----------------------
#org 0x165DBE
textcolor 0x0
msgbox 0x817E67E '"You're a TRAINER, right?\pBROCK's l..."

It reminds me a bit of Skyrim's console commands, and seems easier than Assembly language.
Now for mapping. Experts can easily edit the in-game graphics (graphics meaning tiles). But editing the map itself is quite an easy task. Advance Map (for the third generation) and GoldMap (for the second generation) are fairly user-friendly and may need a few tutorials to help fully understand it.
Some of the original art can be unpleasant to look at, such as Nidoking in Emerald. This can be changed through spriting.
However, changing all Pokemon sprites can be a difficult process, especially with Emerald's animation issue. But some hackers are willing to weather the boredom for recognition.
There are some hacking tools are present for the whimsical, such as the day & night and seasons system. Attack editors let you replace older moves that you never you used with the newer moves from newer generations. Pokemon editors edit what Pokemon learn and what their stats are. Palette editors can edit the colour scheme of Pokemon, so that you can finally see your dream of obtaining the one and only cyan Hypno. You can also change the Pokemon which can be found in different areas and the percentage probability of running into one.
Another thing you can do is make the game more challenging by raising the levels. What's the fun in destroying NPC's level 50s with your level 80s? That's what the Trainer Editor is for.
Patching is a short and helpful process. Patching can translate a Portuguese hacked ROM into an English one. There are also patches that can put newer generation concepts into our older generations; such as indoor running, physical/special split and new sprites. Some patches change font (for the helvetica loving hipsters) and others de-capitalize everything (so your players don't rage-quit because the game was shouting at them).
Hacking tools give you a lot of liberty. Now will you use your hacking for good or for evil? Will you use it to give yourself a level hundred Red Mewtwo at the start of the game? Or will you use it to create the game every poke-maniac dreams of and curses Game Freak for not creating? With geek power comes geek responsibilities.

Check out our reviews of hacked Pokemon games http://bit.ly/1cnBhMp