Like Russell I spend a lot of time on conference calls. Here's my advice.
Use the Mute button. "Signal to noise ratio" is a common electronics' concept. So let's keep the noise floor down so that the signal is easily heard. "Automatic gain control" is another common electronics' concept. Your microphone volume will be raised until there is a signal, and if you aren't talking then that signal will be the interesting conversation on the far side of the office.
Videoconferences are preferred. If you have a regular meeting, then arrange it to use a video conference. This is far superior to phone, but also trickier to set up.
Introduce yourself upon joining. Someone needs to keep track of the quorum, so when you connect listen for a moment and then at the next break in the conversation say "Hi, Jane joining the Blah Conference, muting now" then press Mute. Because the noise floor changes when you connect you are disrupting people when you join, so it's pointless to try to join without announcing yourself, people just wonder "Who was that?" If you've crashed someone who was speaking then because they know you "muted now" they can continue.
Don't be late. Timeliness is more prized on audio and video conferences than in real life. So connect before the clock strikes the start time.
Audio quality matters. A good level of audio, with little background noise, and no breathing noise. You just need one person to mess this up to make a conference a misery. Don't be that person -- everyone is listening to find out who it is that is being so annoying. If you are telephone conferencing then do not use hands free, pick up the receiver. If you are telephone conferencing then use a landline if you at all can.
For both phone and computer conferences a good headset makes a world of difference. A bad headset is worse that no headset at all, so use a good product. I personally like the Plantronics products for both phones and PCs.
If you can't use a headset, think seriously about a good microphone, a small mixing desk, and a monitor-quality set of headphones. I've used this and with almost all conferences people remarked on the excellent quality.
Output audio is important too. If you are using a real conferencing system with echo suppression which works, then put in decent speakers, like those of a hifi system.
If you are teleconferencing with a group of people surrounding a table then don't just plonk the corporate phone in the middle of the table and hope for the best. The Polycom SoundStation has an awesome reputation for this task.
If something has changed, connect early. If you've never conferenced using this facility, connect an hour early. If they've rejigged the conferencing system, connect an hour early. Most systems will let you disconnect and return later.
Have a backchannel. E-mail, IRC, IM, web forum, whatever. Some way to share electronic materials. Jabber conferences make a good back channel. For huge conferences (and the SARS teleconferences had hundreds of people) use the backchannel for people to indicate a desire to speak and for the chair to call them. Also useful in huge conferences for collecting the attendees and apologies. For truly massive conferences pay a typist to transcribe, as there's always one site which will be having difficulty at any one moment. If you find yourself doing all the work in the backchannel then reconsider if this should have been a teleconference or videoconference at all.
Have a pre-filled archive. Use a wiki page. Require people to submit their electronic materials there beforehand (and minutes beforehand is fine). That also becomes a good place to state the agenda and to keep the minutes.
Some additional advice for videoconferences with lots of people:
Videoconferences are preferred. If you have a regular meeting, then arrange it to use a video conference. This is far superior to phone, but fiddlier, so it's really only worth it for regular meetings.
Have a chair. Someone to announce the agenda item. Someone to call on people to speak. The chair needn't be the decision-maker, quite the reverse. In that case the decision-maker can open with "Thank you all for coming, Fred will be coordinating the conference, so please wait until he calls upon you to speak." Fred needs some political nouse so that he calls the correct people in at the correct time and some knowledge of the issue so that he can spot people how are about to make a valuable contribution.
The person calling the conference should have arranged someone to take the minutes. Doing this a backchannel can be useful.
Put your hand up. If you want to speak, raise your hand. When the chair calls on you, then unmute and say your piece.
You are on TV. Come to the point and stay on it. Then get off. Presenting your view clearly is important, so think over what you are going to say. The sort of cultural verbiage which takes place in person can become very boring, Just like when watching the TV, bored people get cynical.
Good audio is more important than video. Get the audio right and the video can be terrible. Get the audio wrong and it doesn't matter how good the video is.
Good images are more important than refresh rate. Use a good camera. Then light the scene well. Zoom the camera so that two-thirds of the screen is full of what is important. So if it's just you then most of the screen is your face.
A lit image is a good image. Your office lighting isn't going to cut it. You need some diffuse lighting coming from behind the camera to stop shadowing your face, this can be simple as a low wattage lamp placed behind your laptop and angled to put light up the wall.
Don't use LED lighting, yet. Light has colour. The videoconferencing system adjusts for this. In theory this is done automatically, but finding the setting and hardcoding it to your lighting technology and your country's AC frequency is a good idea. Unfortunately, there's usually not a profile for LED lighting.
Videoconferences have more things to break. Have a backup plan. H323 and SIP videoconferencing systems which allow people to dial in from the PSTN are great for serious conferences as they readily have a backup plan to failing client video setups -- ring in.
Use an appliance. One of the small videoconferencing units. Or a small computer which isn't your main development machine. I've rarely upgraded my Linux distribution and had videoconferencing applications work without fiddling. That's not usually the applications fault, but the breakage of the Linux audio or video systems or drivers in new and interesting ways.
Have an expert immediately available. Big videoconferencing users will have experts on call. But a medium sized videoconference should have a person who can drop out to solve the connection issues of a party. The availability of an expert makes a huge difference and is the best reason for outsourcing your videoconferencing (and no, not a plug for outsourcing to my employer, rather just what we found we had to do to make a videoconference work when it has many hundreds of people).
You'll notice how little of this has to do with the conferencing technology you use.