Crypto currencies and blockchains in general allow you to work with arbitrarily many accounts at the same time. However often people want to have a default/primary account (e.g. miners have a designated mining address, average users will usually use one particular account even if they have multiple one for other purposes).
Coinbase or etherbase (they are the same thing) is just this. However to keep it simple and less surprising, your coinbase account is actually the first account in your keystore (i.e. in theory the first account you ever created). You can manually set your etherbase to a different account if you reorder them (i.e. rename) in your keystore folder (btw, Geth 1.3.x requires a specific (relatively strange) key naming convention, but 1.4 onward will be able to use arbitrarily named keys from the keystore folder).