Yann Bizeul, the developer of GeekTool, has released version 3.1 of GeekTool via Twitter:
To all : please update to GeekTool 3.1 http://t.co/26vYQwzWWP— GeekTool (@geektool) July 1, 2013
Unfortunately it seems that as the Mac App Store rules have become more strict, Yann Bizeul has decided to stop distributing GeekTool via the App Store.
For the new version to install correctly, stop and remove MAS version first— GeekTool (@geektool) July 2, 2013
To upgrade, you will first need to open GeekTool and disable it. Then find the GeekTool app in the Applications folder and drag it to the Trash. This may require an administrator password. Finally, download and install the new 3.1 version.