That's not a silly question, that's actually a very good question!
I have two definitions for a mod (short for modification), a loose, general one and a strict one. The loose, general one is anything that modifies gameplay by replacing or overriding files that originally came with the game. These would include mods that replace sounds, hilts, or skins that originally came with the game. I would not include maps or skins that add but don't replace game files. So a mod that replaced the protocol droid voice in CTF with Mon Mothma's voice, or a skin that replaced the default Luke skin with something else, or improved map bot routes would be a mod, but an additional map or skin that you could choose to use or not and that didn't replace and original game file would not be a mod. These "mod" files go in the base directory.
The strict definition of a mod means that the command line must be changed with the command "+set fs_game <modname>". The mod files are kept in a separate directory in the GameData directory, separate from the base directory. This would include server-side mods like xMod2, JA Reloaded, JA+ mod, and Disruption, and client-server mods like Asteroids and the OJP mod. There are also single-player mods that can be launched that way or from the Mods menu in the single-player Main menu, such as Melee mod.
A mod can radically alter a game so it's like a totally different game. The Troopers: Dawn of Destiny Mod converts Unreal Tournament 2003 to the Star Wars universe. The Colosseum Mod (
http://www.pcgamemods.com/1945) for Jedi Knight II: Jedi Outcast converts JK2 into a Roman gladiator game (highly recommended if you have JK2).