I just started using Mingle from Thoughtworks and so far I'm liking it very much. Took me a few hours to get the hang of it and then I was able to create a simple tracking application for my simple needs. There are sample templates included but they were overly complex and not what I needed.

What really impresses me about it is how easy it is to make your setup as simple or as complex as your needs are. It's free for <= 5 users and very pricey after that.

It's a jruby on rails app and I'm running it on glassfish on ubuntu.

http://studios.thoughtworks.com/mingle-project-intelligence