Permissions: addresses can be assigned any of the six permissions in any domain. This allows you to directly permission user accounts, or to give permissions to extension contracts that implement their own decision making logic.

Extensions: contracts that are assigned permission within some domain of the colony and implement some logic around decision making/membership.

Reputation: each time the colony pays you in its native token, you earn an equal amount of reputation in that colony. The reputation decays over time. Reputation is used for vote weight in the motions & disputes module. Reputation and native tokens can also give you some economic interest in the colony if it is making use of its rewards pot; a pot of funding that can only be used to distribute tokens to reputation and native token holders.