Where do I get the mods, how do I use them? Do I have to put them in a special folder, if so which one?
Also, people keep saying things like "Oh, _insertnames_ mod _insertmod_ is really good!" and I never see any links, or any way to actually DOWNLOAD the mod...
Don't worry...you just go to a server that has the mod installed, and if autodownloading is enabled, it'll just get the mod for you. When you have a server selected, you go to Server Details and across from Game it will tell you what it is running. (Base, Relics, Domination, etc...base is regular Trem.)
You need the TJW mod to see them I think: http://trem.tjw.org/backport/
You do not need a special client to play on modded servers, you can sort by game either with my client or with a game browser (XGF etc).
See my FAQ: http://risujin.org/tremulous