I have a mod called mod runner. All I know is that you need it in the main folder, and you need patch000.dat (which you normally take out for mods).

So my question is: How do you add mods to the list? I've looked around, and the best I found was just the start of how it works... not adding in mods.

Here's a thread about how to use Mod Runner:
http://www.duckandcover.cx/forums/viewtopic.php?t=4356&sid=7abf5a64e869edbe916704812d9e3888

It seems you just have to place it in the game's directory and put the mods' DAT files in the same location.

lol
That's the site I was alluding to. It tells you how to start up, but not how to do more than that. I tried do what you said, and it didn't work. Thanks though.