There isn't really a program for making a mod. There are programs for making maps, models, textures and skins, but those aren't mods. Mods are something that changes the game at its core by adding something completely new to it or changes something standard. I may buy a texture change of the core textures a mod. Maps and skins are just an extension of the game really. C, the programming language, is really what you use to 'mod'ify
Sorry, just seeing alot of people, including the web sites for this game, calling skins and maps mods, and its starting to irk me.