Update: GeekTool 3.0.2 is now available on the Mac App Store.
The current version of GeekTool doesn't work well in Lion - apparently it doesn't play nice with Mission Control.
If you are running Lion now, you might be interested in downloading the most recent experimental GeekTool version for Lion. The developer, Yann Bizeul, released it via the GeekTool Twitter feed.
If you are using GeekTool in Lion it's definitely worth following the Twitter feed in case there are any more updates, and it's also a great way to send any feedback.