How do I prevent applications from stealing focus when they startup on Mac OS X?

I think you can't :D You can always execute Eclipse in a different desktop though ;)

In case anyone's still looking for an answer to this, I have recently found this article that should shed some light on the possible solutions:

http://reviews.cnet.com/8301-13727_7-20085680-263/keep-applications-from-stealing-focus-when-opening-in-os-x/

Granted, it's from just over a year after the original question was asked, but folks are still looking for the answers to life's tough questions, it would seem.

TL;DR: You can potentially modify the application itself, and add a parameter set to the app's "info.plist", or you can write a script that will launch the app behind other windows. There's a third "option" that basically says that you can have an app stay above others, even while they're launching, but it doesn't necessarily prevent the newly launched app from stealing focus.