Ryujin
Legend
I thought about getting a Chessex mat but didn't like not being able to draw in much fine detail, or not being able to prepare multiple maps ahead of time, so opted instead to get a couple 1" grid easel pads. It's a good solution whether you need to improvise a map or want to prepare something really complex ahead of time. You can fold up the sheets so they're pretty compact and they make for an unobtrusive presence on the gaming table. It's also pretty convenient to write on the map itself, which saves you from needing an extra note pad/device/whatever to track initiative and status conditions.
I'm running my first online game now, a PBP Zeitgeist campaign on a different forum, and when possible I import the maps from the adventures themselves into MapTool (sometimes doing some editing in Paint.NET or Gimp first to remove details like secret doors or details that I don't want to draw the players' attention to until later).
I haven't really found a solution that I really like for creating maps for online use. MapTool is adequate for map creation though, especially if you have a workable library of art assets like CSUAC, but I don't really like the look of the few maps I've produced through MapTool. The other applications I've tried really aren't any better. Even with my limited drawing skills, I'd prefer to be able to just draw my map on an grid paper and scan it in, but I don't have a scanner, and even if I did, unless it were very large I'd probably have to scan most maps in two or more goes, then stitch them together using software -- also a bit of a hassle.
I've downloaded all of the maps available on D&D Insider, as I generally like the art style they employ, and they often have a lot of interesting terrain features, but a lot (most?) of them are from other published adventures and aren't meant to be used directly as battle maps, so many squares are all marked up with areas indicating enemy positions, traps, etc. which is a shame.
There's a relatively easy and effective alternative to scanner, for dealing with large size maps: a digital camera. You can pick up a wide angle digital camera fairly cheaply, create a rig to suspend the camera directly over the map, then shoot it with flash. There are tons of programmes out there that you can use, to correct perspective, and something like a 10 MPix camera should provide plenty of resolution.