I think using Beamer well is hard. Even just getting the layout right is hard - I spend hours moving things around a bit so that the layout aids comprehension. I agree that one should not insert pauses "just because one can", but I think one should insert pauses because it helps people understand what is going on, as if one were writing it gradually on a blackboard.
My top tips would be:
Use pstricks for diagrams, because then you can increase the thickness of the arrows, and pause in the diagram so that it can be built up gradually. There is some kind of myth out there that you can't go through postscript with beamer; this is untrue.
Keep a running frame number discreetly (eg bottom right) so that you know where you are in terms of timing. However do not show how many slides there are in total, so that if you run out of time you can abort your talk without anyone knowing.
Keep the section heading at the top of every slide so that the audience knows where they are. Apart from this and the page numbers I remove everything else like Tom does, but I disagree with the total blankness approach.
Read out every word on your slide. If you don't, the audience will do it in their heads anyway, and won't listen to you while they're doing it. This is also why pauses are good (otherwise the audience will read to the end of the slide and not listen to you), and having the rest of the text in light grey before it has officially appeared is something I find extremely counter-productive.
I personally hate sans serif font for maths presentations but I seem to be the only person on earth who does. I find it extremely difficult to read from far away.
I prefer to keep the lights on the audience. It might make your slides more legible if you dim them, but it will make your audience fall asleep, and will mean they can't write their own notes or do their own work when they're bored, which is just cruel. Also, if you dim the lights you won't be able to see them, so you won't be able to communicate with them.
Personally I think the standard font size on beamer is too small, and I take it up by a point or two.
I agree with Tim Gowers' point about copying material you need again instead of flicking back through the beamer.
Purchase a Kensington remote page turning thingy with laser pointer. It's not that expensive (under 30 quid) and works extremely well. It's better than relying on your hosts to provide one, and we've all been to talks where the speaker can't work the remote page turning thingy. So it's better to have your own, which you know how to operate.
I have never read the manual. I assume I can do anything I want, and look it up when I need to. The manual is epic and I would probably reach retirement before making it through.
I try to avoid any text that has to run over one line; I think that indicates when my sentence is too long for a presentation. The one exception is if I'm saying something informal, like a slogan, idea, or moral, in which case I put it in a box.
My top tip for actually writing the beamer is to plan all the slides first on paper, then type in the material without any thought about layout, and then go through and sort the layout out separately. These three stages require different types of brain function and it's hard to think about them at the same time.