I hacked together an utility plugin for BatClient.
You can find the pre-alpha-alpha-no-whining-0.1 version from here:
http://www.fizzl.net/batmapper/

Currently you can insert single characters into a grid, add mobs as lines and add custom notes.
data is saved as java serialized objects.
Exporting to a textfile is in high priority.

Data file compatibility will most likely break between each version, so um, dunno. Don't use this for anything :P

I did some pondering, and decided something rather important.
I will stay with the current data format until version 1.0. This will force some limitations, such as no extra fields to mobs and the map size will be fixed to maximum 50x50 untill then.
When I will break the format, I will switch to sqlite, xml or other such easily transportable and mutable format and create a converter to import you old areas.

What I wish to achieve with this, is to lure some of you to actually use the plugin so I can get some feedback while developing.

This I cant promise since Im still a tf user, BUT I've done an automatic mapper for tf (took me 2 years). It uses mysql. I'd be happy to discuss any issues you may have with this project. There are a lot of screwed up maps out there waiting to be mapped... :)

I think this is a great idea. I downloaded the plugin, and one of my first thoughts while using it was how I didn't want to invest much effort in maps if they would be obsolete with the next version.

Mechanics question: how do you make the window reappear if it has been closed? Only apparent way right now is a client restart ...

Currently there is not way to relaunch the window. I think I need to make a script file and support for reloading the window if it is closed. I am hoping in some future versions of batclient plugins could register menu items from the main 'settings' menu.

Years back, I tried to configure zmuds mapper but gave up in frustration after some time.
I think I could make an automatic 'following' mapper that would create roooms and connections in memory. However, I have no competence to start pondering how to actually visualize the map in meaningful manner reliably.
Have you already solved the latter problem?

Oh yeah, v0.2 available. It includes the export function.

Well, the problem with automatic mapping is that in case of problems you always need user intervention.
On screen I visualize the map like clairvoyance does. In memory I just use a grid. For the grid to work you need a list of rooms, their exits and to which room each exit leads to... its pretty complicated but with overlapping and mazes it gets even more complicated.

See an example to see how in Sunderland the exit w sw from the player (P) can cause overlapping. I'd leave that overlap detection to the user and let him "stretch" the exit by himself? I'd also leave maze detection to the user since thats pretty complicated too (one has to examine room descs, exits and still not be sure if youre in a maze or a lazy coder's cloned rooms).

I seem to have lost access to my created maps. Is there some way to reload/recover them using the .area files?