Having just grappled with modding X3: Terran Conflict, I can safely say that modding seems easy to someone who's already done it, but if you've never modded, or you've never modded that specific game, then it doesn't make much sense. For instance, with X3:TC I grabbed a few mods that had readme's in them, and the entire instructions were "Installation: Instal the mod as normal."
Minecraft modding happens in one of two ways. Most mods work with Forge now, which is infinitely easier and easier to deal with. Forge will add a folder in your .minecraft file named "mods". Simply drop the mod in there, it's usually a .zip or maybe a .jar or sometimes just a regular folder. Place it in the \mods folder and boot up. That easy.
But many mods are a bit deeper than that, and Forge doesn't offer enough access, so they go for direct modding. For these, you open the .minecraft folder, then go into \bin and then fine "minecraft.jar" - right click it and "open with" 7zip or winRAR Archiver - I prefer winRAR, even if it tells me to buy the full version every time I open it. Open the mod you downloaded, it's usually packaged as a .zip so just open it, you don't need to actually unpackage it anywhere. Click in the mod's package, hit ctrl-a, and drag into minecraft's package. If it asks you to replace any existing files, then agree to all of them.
Or simply: Forge mods are dumped in the "mods" folder. Other mods are dumped into minecraft.jar directly.