Eclipse's own solution is working sets, however I still struggle with plugins, sometimes it just seems overkill to have Android, Java, C, Ruby and others all together in one huge immutable installation.
In the end I decided to simply have multiple Eclipse installations.
One folder for each project and dependencies. One clean, movable folder. Other projects have different folders, and occasionally - when they share code - subversion/git do the trick and one project can be on multiple eclipses.
I find this works for me the best, but let me know what you think.