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: 
You can use the last part of each lines in `.ssh/authorized_keys` is intended for comments. From `man sshd`: 

> 
> Protocol 1 public keys consist of the
>  following space-separated fields:
>  options, bits, exponent, modulus,
>  comment. Protocol 2 public key consist
>  of: options, keytype, base64-encoded
>  key, comment.
> 
> 
> 

And to answer the question, I use `vim` but any editor should do it.

My comments usually contains:

* creation date
* physical location: creation computer / USB stick (I prefer not to move private key but generate/revoke them and know where they are)
* 1-2 words about purpose (for which login, for which client, for which script)
Bastillion - <https://www.bastillion.io>

Users manage their own SSH keys based on profiles that have been assigned to them.

<https://www.bastillion.io/docs/using/keymanagement/>