Question: I have a server with multiple users which each have multiple authorized SSH keys. Is there any effective way (command line utility?) to keep track of which key belongs to who and to quickly remove/add keys (apart from ssh-copy-id)?

Answer: 
I'd checkout the [Monkeysphere](http://web.monkeysphere.info/) project. It uses OpenPGP's web of trust concepts to manage ssh's authorized\_keys and known\_hosts files, without requiring changes to the ssh client or server.
There's also [`ssh-import-id`](http://manpg.es/ssh-import-id), which can securely import users' SSH public keys from [Launchpad.net](http://launchpad.net).