Edit: The "anvil" branch is now merged into master as version 0.9. The note about using anvil is still relevant, but there no longer exists an "anvil" branch. Links to the docs updated. -brownan
The Overviewer now has initial support for the new Anvil map format (used in Minecraft 1.2)! You can find this version in the anvil branch on GitHub. If you need a Windows build, feel free to ask us in our IRC channel.
(Edit: we build the windows builds on-demand. Right now things are developing rapidly and the current version may be unstable, so that's why we're not building them automatically. Once things stabilize we'll start posting the new builds on to the github downloads page. -brownan)
Using the Anvil Branch
The Anvil branch is based on our recent code rewrite, which means that it has a different configuration format and command line options. Please see our blog post or the documentation for more details. Changes made during the rewrite made it much easier to upgrade the Overviewer to Anvil; making these same changes to the old code would be much harder, so we are not planning to update the old code to handle Anvil.
Due to the large changes made to support Anvil, you will need to render your maps from scratch. Trying to update existing maps will not work. Also, due to major changes to the web assets during the rewrite, you should not simply copy over custom web assets to the new version. In particular, custom overviewerConfig.js files can cause strange problems.
A Note about Biomes
In addition to the much taller worlds possible with Anvil, the new map format now stores biome information with the chunks. This means that you no longer have to run the Biome Extractor in order to get biome colors on your maps. Biome colors are working right now in the Anvil branch; go check it out!