We use a message board and googledocs.
The message board is good for scheduling games, planning the party's next move (do we head north into the mountains or south into the desert?) and light in-character stuff between sessions.
We use a googledocs spreadsheet to keep track of everybody's skill bonuses, loot, powers, etc. In-game, if I need to know the wizard's passive insight bonus, I can check it on the spreadsheet without tipping anyone off that something fishy might be going on. Out of game, I put whatever treasure the party found in the spreadsheet, and the PC's can fight over who gets what.
Googledocs also has PowerPoint-style presentation software. I've been using that to keep track of maps and pictures relevant to the current campaign.