Ubuntu :
Set required environment variable inside /etc/environment and restart the machine. This will set environment variable which can be inherited inside eclipse workspace. Above method will set the environment variable for all the users. To set environment variable for individual user set the required variable inside <user home>/.profile file. While doing so please make sure you use export keyword before variable. Alterante option to use .bashrc to set those environment variable, here as well you need to prefix export keyword.
Note: here is some issue to set D_LIBRARY_PATH through /etc/environment refer for workaround.
MAC OSX : (tested on maverick): Set required environment variable inside /etc/launchd.conf (setenv PROJECT_HOME <Project home location>) and restart the machine.