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By now, both Python and Java's implementations are reasonably mature and solid, and their functionalities are quite 

 the same (I don't think it's quite 100% equal yet, but moving in that direction). So, if you already have knowledge of any one of these two languages, you should just go for it.

And if you are a beginner or one who does not know either of them and want to try the non-Java languages that are (more or less;-) supported on the JVM side of GAE ( This includes Scala, server-side Javascript, JRuby, etc), then it's worth trying.

If you prefer a complete development environment including IDE support => Java

If you need the most advanced features of App Engine => Python
