Be patient and don't assume a colleague is available just because the person's status indicates s/he is logged on. Your colleague may be busy or engaged in an important task. You may want to include in your message when and how the other person can reach you.
On the other hand, and within reason, be responsive in a timely fashion. When possible, advise the sender that you are currently busy and will get back to him/her as soon as possible. Set expectations.
If you plan to walk away from your workstation in the middle of a chat, please advise the other person that you will be right back. If you are not in the middle of a chat, the correct practice is to change your status to "Away from workstation".
Although instant messaging is considered less intrusive than a phone call, it still can distract the recipient of the message. To mitigate this potential side effect, show restraint when sending multiple messages in a short period of time.
Keep your messages succinct. If the length of your message looks like an email, then maybe it should be an email or even a phone call.
Be watchful of who is your intended recipient, especially when you are conducting multiple chats.
Tread lightly when using humor or sarcasm, since these can be misunderstood or have an unintended result.
Don't SHOUT (all caps) or use too many emoticons. These can be annoying.
Don't send angry or offensive messages. See UCSB Electronic Communication Policy - http://policy.ucop.edu/doc/7000470/ElectronicCommunications