Pakscape is a program that lets you open up the .pk3 files and that lets you create your own .pk3 files for the game.
You need it for your mods and maps to work properly.
You basically create directories in your .pk3 file that the game uses to run your mods and maps. That's why, if you notice, when you download mj/m/s they are always .pk3 files.
You can get it here, along with a quick tutorial on using it:
http://www.dafront.com/~nemesis