In addition to waht jeffMOD said:
Making mods is quite easy.... Actually wrong. It's rediculously hard. But setting it up, That's easy:
Part 1
Part 2
Part 3
Part 4
Or you can download a mod from the vault, and copy the folder layout, and modify any icons.. sounds.. etc..
As for programs:
Hammer
Model viewer
Sprite Viewer
Wally - Exporting to .wad
Photoshop / Paint.net / GIMP - creating textures
Compilator - Compiling made easy
As for decompiling:
Don't do it unless you want information on entity set ups. Even that's a last resort because the internet / TWHL is vast with information. You can even jump on IRC.