The correct, simplest, and most robust way to do what you want is to use a version control system like CVS, svn, git, etc. Even when working alone on a project, its a wise idea, not just for having the code on different computers but also because it gives you all the benefits of version management like being able to rollback changes, etc.
There are many free or inexpensive cvs, svn, and git hosting options; I strongly suggest you get an account and check your code in/out on the two machines you work on. If you have a web hosting provider, chances are they provide one of these services with your account.
If you're going to insist on manually moving/syncing code, you need to know that Eclipse workspaces are NOT designed or intended to be shared. Trying to do so always leads to headaches and other pain. Instead, you can export/import the project(s), not the workspace. Keep in mind that in Eclipse, a Project does not have to be located in the workspace directory; when you create a project there's an option to store it in any arbitrary location on your filesystem. Also note that all files under the project (including .project and .classpath) should be shared, except generated stuff like bin/ and gen/. This applies to using cvs, svn, etc or some other manual syncing mechanism.
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