You can create Eclipse "Links" in your project which can point to other locations outside of
workspace or project location itself. They are similar to unix soft links. 
You cannot create relative links, however you can create links based on "Linked Resources Variables"
(starting from IDE 4.6). 

For example you have a project aaa and you want to link output folder to somewhere else in file system,
for example to /opt/sources/output, we will create variable SOURCE_DIR pointing to /opt/sources that all projects can 
share.

* Select "New Folder..."
* Click "Advanced..."
* Check "Link to folder in the file system",
* Select "Variables..." 
* Click "New..."
* Enter name and location in file system for this variable, click OK.
* Select "Extend..." and select "output" folder (from /opt/sources).

Now your link would look like SOURCE_DIR/output. Click Finish.

To enter or view list of Linked Resources Variables open Window->Preferences->General->Workspace->Linked Resources.

Links structure is stored in .project file in the root of your project. Linked Resource Variables are user specific and 
stored with local workspace settings.

Read more about project structure example here: http://community.qnx.com/sf/wiki/do/viewPage/projects.ide/wiki/
ProjectsBuildAndIDE