This seems to be the supported native method in OS X:

cd /Applications/eclipse/

open -n Eclipse.app

Be sure to specify the ".app" version (directory); in OS X Mountain Lion erroneously using the symbolic link such as open -n eclipse, might get one GateKeeper stopping access:

"eclipse" can't be opened because it is from an unidentified developer.

Your security preferences allow installation of only apps from the Mac App Store and identified developers.

Even removing the extended attribute com.apple.quarantine does not fix that. Instead, simply using the ".app" version will rely on your previous consent, or prompt you once: