After some discussion with a colleague from another company that also uses App Engine, he told me that he managed to cut down his app warm up time from ~15 seconds to ~5 seconds
What we did in Eclipse was:
You can configure the jar builder to execute automatically as class files change (which in turn are usually automatically recompiled as your source files change).
There are some downsides, though. For some reason the google eclipse plugin gets confused by your changing the output directory of the java compiler. This means you will have to manually point to the war directory when deploying, and I believe you'll have to manually copy some GAE jars into the war/WEB-INF/lib folder.