As I wrote in another post, using a BAT file to compile using MSVC is a very bad idea - you'll miss all the debugging info, runtime warnings, such as unassigned variables, asserts etc. It is good enough if you want to compile MS for yourself; it's useless if you want to develop. A project file is the only way to go.
I managed to fix up CMakeLists.txt for use with MSVC2008 - now it generates proper project files for the main exe and the plugins; though the output paths may still need some tweaking ($/files/Debug, $/files/Release). Since I'm not yet friends with Git, I'll try attaching a diff file to this thread so that anyone interested can try and review it.
I think CMakeLists is well suited for MineServer, it seems simple enough that even I managed to learn to hack it within a few hours, and it's being done already, more or less.
On a similar note, the wiki needs serious care with windows compiling. If my CMakeLists patch (or a derivative that works) gets into the main source tree, I can write something up.