We have a a product developed on Windows for years. The product is composed of one Eclipse workspace and about 20 projects. On Windows, we ask every developer check out proj
I develop an Eclipse based product for Mac and WIndows (haven't tried Linux).
The solution I found to work best is to actually go and manually check out the projects in the workspace on each machine directly from source control. While the project structure does convert between platforms, any attaches, such as version-control stuff does not. I am not sure why, but I guess each thing has its kinks. You may be able to able to hasten things a little by creating a project working set (or whatever it's called, I think it's a PSF file) for a platform, and then reuse it on all platforms.
Another problem is that Eclipse versions are not 100% compatible. One of the problems I have is with manifest files for plugins, which have different semantics (e.g., what to do with exported packages that don't actually exist) in each platform, causing a headache.
Finally, be away that Java on Mac and PC are not identical. In fact, Eclipse has two versions for the Mac. I usually end up running and compiling on Java 5 on the mac, which does have some incompatibilities with Java 6.