After upgrading from Ubuntu 12.10 to 13.04, I had this problem.
As it is usual case with eclipse "eclipse.ini" was the point of issue.
This file can be found in /etc/eclipse.ini .
Here are the contents my eclipse.ini file:
####################################################################
-startup
plugins/org.eclipse.equinox.launcher_1.2.0.dist.jar
--launcher.library
plugins/org.eclipse.equinox.launcher.gtk.linux.x86_1.1.100.dist
-showsplash
org.eclipse.platform
--launcher.XXMaxPermSize
256m
--launcher.defaultAction
openFile
-vmargs
-Xms1024m
-Xmx1600m
-XX:MaxPermSize=1024m
-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=/usr/share/eclipse/dropins
####################################################################
So first test was to check existance of org.eclipse.equinox.launcher_1.2.0.dist.jar
and org.eclipse.equinox.launcher.gtk.linux.x86_1.1.100.dist on system.
Upgrade replaced these files with newer versions.
So fixing this issue was as simple as changing names of these files to match newer version.
New contents my eclipse.ini file
####################################################################
-startup
plugins/org.eclipse.equinox.launcher_1.3.0.dist.jar
--launcher.library
plugins/org.eclipse.equinox.launcher.gtk.linux.x86_1.1.200.dist
-showsplash
org.eclipse.platform
--launcher.XXMaxPermSize
256m
--launcher.defaultAction
openFile
-vmargs
-Xms1024m
-Xmx1600m
-XX:MaxPermSize=1024m
-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=/usr/share/eclipse/dropins
######################################################################
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