You know, for the project we created (a sort of IRC chat, simplified), I made the choice to not use Eclipse at all. Things wen pretty well once I had my Makefile setup ! Just take a look: jirc. Fork it, "make" it, run it. I like how simple it make the whole process. And of course, it is Eclipse compliant (I didn't want to forced my mate to go without Eclipse like me. Ah, freedom...).

Also, I learnt A LOT by building this Makefile. Why would you care about what a classpath is if Eclipse handle it for you ? How do you deal with packages if nobody does this for you ?

IMHO, it's okay to use any automation tools. But you must consider doing it only once you tried to do it by hand, so that you know what you are delegating.