Video Conferencing Guide

By default, mute your microphone when you are not speaking.
Headphones almost always fix feedback issues. If you hear feedback of any sort (even if it appears to be occuring at a different location than where you are) then you should put on headphones. Sennheiser makes a great pair of cheap over-the-ear headphones for $20. Good noise-canceling headphones are a gift from heaven.
Every room needs only one set of speakers and one microphone. Under normal circumstances, there is no need to have two laptops in the same room connected to the same videoconference.
Pay close attention to the messages in the chat room. It is an incredibly helpful place to communicate when there are audio problems and sometimes useful for the host even when there aren't audio problems. It is also a great way to moderate communication when several people would like to talk at once.
In each room, arrange the camera (e.g. on the laptop) far enough from the speakers to ensure that the video catches the faces of the audience in the room as much as is possible. Sometimes this means you need to reconfigure the chairs and tables properly. I've spent entire videoconferences talking to an unmatched pair of shoulders with a blank chalkboard in between them. (One problem I've encountered here is with Facetime and iPad docks. Facetime doesn't seem to be compatible with some docks, so it refuses to properly orient the video as long as the iPad is docked.)
Obviously, the conference is limited by the speed of your internet connection, so be prepared to turn off video if one or more of the participants is on a limited connection
Hosts: plan to arrive ahead of time to help your users test their audio connection. Participants: arrive early if you think you might have problems.
Note that laptop microphones often pick up typing, so if you're using your laptop microphone be prepared to be unable to get any work done during the meeting when your microphone is on. Physically moving your laptop when your microphone is on can also cause quite a bit of noise.
Audio problems can often be diagnosed by the host when they can see who's microphone is transmitting a signal to the entire group. Ventrilo and Teamspeak are very good at allowing the host and users to see and manage audio signals (but also may require more technical expertise on the part of the hosts and the users). Zoom and Adobe Connect are sort of middle of the road. Skype, and Facetime are horrible for this, as their interfaces are designed to be very simple, at the expense of giving hosts good methods for diagnosing audio issues (so far as I know).
Do be careful about playing audio or video on your computer during a videoconference. Enough said.
Feedback is caused by a microphone picking up the audio signal from a speaker and then sending it back to the same speaker. Chat and video software can reduce feedback, but the software correction can only help so much, especially if the microphone is pointed at the speaker.