I've been using eclipse for a long time to do development. One of the problems I've come across when working on other people's projects is if they come from source control, some of the eclipse project files "default.properties" and other xml config files are missing. Its usually a big pain in the butt to get the project running in eclipse. I understand the reasoning to not have certain files tracked because they may be full of specific stuff to a certain eclipse install. How do all of you manage that?
My solution has always been to not check those files in.
I really have never liked it when I do a check out and have to filter through all the IDE-specific stuff. Why not use a common ground? If the IDE files are the common ground, great. But, more often than not, something like Ant and Maven are the common ground.
It depends on the audience, but I generally avoid it. Build tools are mostly universal, and IDE's fall near the edge of the text editor religious wars. I'm a peaceful guy and practice my religion in private.
I would typically check those files into source control. It's usually best to check in everything you need so that you can simply check out a fresh copy, fire up your IDE and build.
It's slightly different if people are using heterogeneous IDEs and build tools (e.g. if some people are using Eclipse and some are using NetBeans) but that's a situation I'd generally try to avoid.