How do you kick a benign user off your system?

There's probably an easier way, but I do this:

1. See who's logged into your machine -- use who or w:

   > who  
   mmrozek  tty1         Aug 17 10:03  
   mmrozek  pts/3        Aug 17 10:09 (:pts/2:S.0)
   

2. Look up the process ID of the shell their TTY is connected to:

   > ps t  
   PID   TTY      STAT   TIME COMMAND  
   30737 pts/3    Ss     0:00 zsh
   

3. Laugh at their impending disconnection (this step is optional, but encouraged)

   > echo "HAHAHAHAHAHAHAHA" | write mmrozek pts/3
   

4. Kill the corresponding process:

   > kill -9 30737
   

---

I just discovered you can combine steps 1 and 2 by giving who the -u flag; the PID is the number off to the right:

> who -u
mmrozek  tty1         Aug 17 10:03 09:01        9250
mmrozek  pts/18       Aug 17 10:09 01:46       19467 (:pts/2:S.0)

As Micheal already pointed out, you can use who to find out who's logged in. However if they have multiple processes, there's a more convenient way than killing each process individually: you can use killall -u username to kill all processes by that user.

Necromancy!

I appreciate the humor of the accepted answer, but professionally I can't advocate it.

The most graceful method I'm aware of is to send a -HUP to the shell to simulate a user hangup. You can send this to the user's idle sshd to simulate their connection being lost, which triggers a cleanup of the entire shell environment (including child shells), or send this to specific nested shells (say, ones setting inside of a disconnected terminal multiplexer that are keeping you from unmounting a filesystem) if you want to be really precise.

Using write to send messages to terminally idle ptys before you boot them is a fun hobby though.