Where they come from: killing zombies. Every kill pays a few, and the rate goes up with your rank and donor tier.
What they buy: teleports (/home, /trader, /waypoint), items on the player market, bounties on other players, and everything on the store page - build kits, prefab bases, pit dig-outs and nukes.
This is the main currency. If you only ever earn one, earn this one.
Where they come from: meat. Put raw meat in a registered Trader Crate and run /convert - it turns the meat into tokens. Hunting is the only way to earn them, which is the point of them being separate.
What they buy: animals. /tame claims a wild animal as your pet, and /heal patches one up after a fight. Both cost tokens and nothing else does.
If you do not keep pets you will never need these. If you do, they are the difference between a bear that follows you and a bear that does not.
Zombies pay Knight Caps. Animals pay Meat Tokens. Caps buy things, tokens buy company.