Usually we use Photoshop for projection and either use maps straight from the publisher (Wizards maps, Paizo supplements) or build them from scratch with Dundjinni.
We used to do conceal layers but it got to be a pain.
However sometimes we pull out either a battlemat and markers for large open areas or the Mastermaze for smaller grids that need a little more spontaneity.
One of the DMs used Campaign Cartographer, but using CC and Photoshop with reveal layers got carried away with the fiddling to the detriment of playtime (messing with spell radius, computerised rangefinding).
For spell areas I recommend Steel Squire templates.
We used to use custom Excel for character sheets but I find them slower than paper sheets with a note pad. It has been my observation that characters on the laptop don't get touched between sessions.
They are likely to not have recorded XP, gold changes, loot splits and seem to only get updated during play time. Basically having characters on laptops doesn't improve time spent during the session - if anything it offers great distractions (not universal but common IME).
Using chat software for notes was also a distraction - probably because our group was never into note passing in the first place.
Lots of space to put books/character sheets 
Plus the LCD idea is pretty sweet, just make sure you mount the plexiglass as close to the screen as possible.
