I'm running a PbP over at Circvsmaximvs.com, and have for a little over a year now.
It's been a great game.
I'll probably repeat a lot of the advice already given, but that's because I didn't bother reading this whole thread.
1. Roll as much as possible for the players. I roll initiative for everyone. And if you want a diplomacy check from the bard, feel free to roll it for him, and then just adjust the conversation as necessary.
2. Keep a bookmark to all the PCs character sheets so you have easy access to them.
3. Use
Home for all your dice rolling needs.
4. Use Powerpoint for battle maps. You can create a square grid map (I LOVE Skeleton Key Games' e-adventure tiles), and there are others - Wizards site has some downloadable ones as well. Or make your own- it's not hard. For example, find a grass background, and then lay over a grid on top of it. Voila - instant battle map for an outdoor battle. Use the PCs portraits as their icons. Powerpoint works great for this because each picture is a separate object, and doesn't become part of the map when placed onto it. So, you can freely move the characters and monsters around without disturbing the underlying map.
5. If a PC performs an action that would probably require a skill check, have them make the skill check at the same time - train them not to wait for you to come back and say "Give me a spot check", or "give me a bluff check". In other words, don't let the players get away with stuff like "I'll try to convince the guard that I have an appointment." and be done with it. Players know the routine. It speeds up play vastly if, instead they say, ""I'll try to convince the guard that I have an appointment. And my roll is a 13+4, for a 17 total." Otherwise, see rule #1.
6. Feel free to make prodigious use of images. The PbP format lends itself well to embedding images. I like to find images of all the important NPCs, and I include them (with imgright tags) in their speech. It gets a little overwhelming to do it everytime, but I like to do it often. Also, feel free to use different colors for different NPCS speech. I use red for the mayor, and purple for one of the NPCs, for example.