My quick reference for IRC commands Quick handy guide to get you started in IRC quicker, or learn something you didn't know. Also includes info on channel and nick registering.
Also, commands that have parts with [] denote arguments that are variables, meaning you put in what you want without the [].

Command syntax What it does
/me [say]

Does an description/action line like this:
*[yournick] describes/does stuff!
In Trillian 0.x, if you use colors, you must use the next command instead

/describe #[channel] [say] Same as /me, only to a specific channel. Mostly used for scripts or if you're using Trillian 0.x still
/nick [name] Changes your nick on the current network.
/list In IRC clients, this gives you a list of all channels on a network that don't have +s or +p channel modes set. Opens in a new window.
/query [nick] Opens a Private Messaging conversation with someone in a new window.
/msg [nick] [say] Similar to /query but doesn't open a new window unless they reply in the query window.
/whois [nick] Gives you some info on the nick.
Put the nick twice to see idle time of people on servers other then the one you are on.
/whowas [nick] Checks for a previous existence of a nick on the server up to a day usually.
/ctcp [nick] [option] Options- TIME: get's nick's local time
PING: Pings selected user
VERSION: tells you what selected nick is using to connect to IRC.
/quit [msg] Logs you off IRC. Msg is an optional parameter to provide a quit message.
/part #[channel] Leaves a channel.
/join #[channel] Joins a channel.
/help Some servers support this command; it gives you a wide variety of info on user and channel modes.
/ns info [nick] Gives you more info on a nick, including contact info and URL (if set)
/away [msg] Marks you as Away. Use this same command with no message to reverse being marked away.

Nick Registering Info
Registering a nick allows you to 'own' that nick. You can set a bunch of options on them, I list recommended options here.

/ns register [pass] [email] Command to register it. Some networks don't require a valid email, but it's recommended that you do. Also, some networks might not allow certain domains.
/ns identify [pass] Identifies your nick.
/ns ghost [nick] [pass] If someone is using your nick, this command will kill them from the network, releasing your nick for you.
/ns set kill on Turns on nick kill
/ns set secure on Turns on nick security. Combined with Kill, gives 60 seconds to identify otherwise the network changes your nick.
/ns help set Gives you more options, like setting a URL, ICQ, etc. for your info
/ns update Updates yourself, including any modes if you don't have them, last seen time, Vhosts, etc.

Channel Registering info and other op commands
Info for channel registering. As usual, I didn't list all the options on here, just the most useful ones.

/cs register #[channel] [pass] [description]

Register the channel. You need to be on it first.

/cs set #[channel] keeptopic on Keeps the topic on even after all users have left a channel
/cs identify #[channel] [pass] Identify to founder-level access
/cs halfop [#channel] Self-halfopping +h on yourself. #channel for one channel only.
/cs op [#channel] Self-op for any channels you're on auto-op list for. Adding a channel name does it only for one channel.
/cs owner [#channel] See above only for +q owner mode
/cs protect [#channel] See above only for +a admin/kick protection mode
/cs voice [#channel] See above only for +v voice mode
/cs [vop|hop|aop|sop] [#channel] [add|del] [nick] Add or del[ete] someone from automatic voice, halfop, op, protected op respectively.
Additionally, using add when someone is on one list will move them to the target list.
/mode #[channel] (+ or -)[mode codes] [nicks] Channel controls. Nicks is only used if it's a mode applied to a user (like +-v) + is apply; - is remove. Modes and their effects are below.
/topic #[channel] topic Changes the topic of the channel.
/cs help Additional stuff you can do.

Mode list
Modes. Nothing more, nothing less. Note that not all of these are on all servers.

Mode letter Effect
+a [User] Sets as an admin (protected) user. Only +q owner can kick, otherwise this has no extra priveledges (that I know of) that an op would.
+b *!*@* [User] Sets a ban on a person or I(S)P. They can't join nor send messages to channel. Use before a kick if necessary (which it should be unless you like to ridicule them).
+c Stops messages containing colors codes from being sent to channel.
+f [xt]:y Flood control. Kicks someone after y number of lines in x seconds.
+h [User] Sets a user as a halfop (%).
+i Marks channel as invite-only.
+k [pass] Makes it so you need the pass you used when setting the mode to get in. You also need the pass to unset the mode.
+m Marks channel as moderated (Only Voice and up can talk)
+M Similar to the +m above, only it also lets registered, identified nicks talk as well, voice or no.
+n No outside messages
+N Nick changes are not allowed when in the channel
+o [User] Gives user operator status (@)
+p Private Channel (basically similar to +s)
+q [User] Gives user owner status.
+r Means a channel has been registered
+s Marks channel as Secret (can't be seen by /list or /whois)
+t Only Halfop and up can change topic
+u 'Auditorium Mode', meaning only ops show in the /names list of a channel you aren't on. Only channel owners can set.
+i Invisible. If someone is not on a channel with you, they can't see you. Trillian sets this by default, but most others don't, you have to set it yourself if you actually want it.
+p A variation of +i above, this hides ALL channels, +s or not, from your /whois
+x Hides your IP address. Preset by most servers.
+r Shows you have identified for your nick