The Best and Only way to manage your mod files.

JoneSoft Generic Mod Enabler (JSGME)

Most Mods are in the following formats, ZIP, RAR, 7z
You can download the compression tools at the following links.

ZIP: WinZip Link
RAR: WinRAR Link
7z: 7z Link

U-Bones has a very useful article about installing Mods that don't come with a readme for instructions here.