/whois [user name] - (eg /whois bob). This looks up some information like their account number (I never knew why you would want to know this) and where that person currently is.
/whisper [user name] - (eg /whisper jim) This is the whisper command. It lets you talk to people without others listening in. Great for arranging games with a password when you don't want it to be gatecrashed.
/who [channel name] - (eg /who Starcraft 1) This gives you a list of all the people in that chatroom. The operators will be in brackets.
/squelch [user name] - (eg /squelch macckee) This is a sort of mute. It ignores messages coming in from the person who you squelched so you don't have to listen to what they are saying. Great if they are shouting abuse at you.
/unsquelch [user name] - (eg /unsquelch macckee) This lets people who you have previousley squelched speak again.
/join [channel name] - (eg /join Starcraft 1) This command lets you join a chat room without having to go to the channel select screen.
/rejoin - This puts you back at the last channel you visited. It also puts you at the bottom of the user list.
/stats [user name] - (eg /stats Littlebeamer) This tells you how many wins, losses, and dissconects in both ladder and in normal games the user has had.
/designate [user name] - (eg /designate yoleney) This gives over the operator command to that person when you step down and resign.
/resign - This is a command to step down as a operator and become a normal user again.
/kick [user name] - (eg /kick tewkeneny) This kicks the specified person out of the chat room but can only be used as a warning as the user can come back at their own will.
/ban [user name] - (eg /ban hogkijer) This bans that person from the chatroom and they cannot return until the operator that banned the person resigns. This is very powerful and is not best used just for the hell of it.
/unban [user name] - (eg /unban hogkijer) This lets that person back into the chat room.