1. Talking clearly, near to the phone - especially in a large conference room with many people around you and many more on the phone line. If you're nowhere near the phone, get closer. If you're near the phone, face it. If you're speaking, remember someone is listening from very far away and the clearer you can make your presentation, the better it will come across.
2. Skip inside jokes; they don't translate well. It's all fun and games until someone can't understand you. I sit on conference calls that are mostly inside jokes and laughter for about half the call. This is great fun for those in the conference room at the other end of my phone line, but I miss most of it. If you have an inside joke, wait for later, or let everyone hear it. This also cuts down on extraneous jokes that really aren't appropriate.
3. Conference rooms should have closed windows. This is a significant problem with conference calls during the summer when construction is everywhere and it's hot in the building. The sirens, the traffic noises, and construction noises really come across louder on a phone line if the windows are open in the conference room. If you have to open the window, crack it and if that gets so loud outside that even you can hear it, remember the people on the phone can hear it more. Close the window until at least the main part of the presentation or meeting is complete and then get some air. Air conditioning is also a novel idea for conference rooms. Hint, hint.
4. Introduce yourselves and let people on the phone introduce themselves. Then use your name each time you talk for a few rounds. "This is Mark, can I ask a question?" This helps the people on the phone and in the room realize that you are speaking to them too. This also helps to cut down on confusion as to who's talking as well.
5. Ask the people on the phone if they need any clarification. Every ten minutes or so, just stop and make sure everyone both in the room and on the phone are tracking the meeting. This is helpful, because many people on a phone line aren't sure when to break in to ask you to speak up and if they don't ask, no one in your conference room will have a clue that anything is amiss. Check in with everyone often and that should clear up any lingering issues with regard to hearing and comprehension.