I've suffered more from this running Eclipse Indigo on a Natty Virtual Machine, but I occasionally get it on my bare metal desktop too. Basically you'll be merrily hacking away and Eclipse will suddenly crash. Hard. It's as if the application window has entered the Bermuda Triangle.
There is some trace though, a hs_* dump file in your home directory. In that file is a message (along with a lot of other verbiage) like this
# Problematic frame: # C [libswt-pi-gtk-3659.so+0x3c17e] Java_org_eclipse_swt_internal_gtk_OS_GTK_1ACCEL_1LABEL_1GET_1ACCEL_1STRING+0x0
Not really helpful but it helped google lead me to a solution. That solution is here: https://bugs.launchpad.net/ubuntu/+source/openjdk-6/+bug/789123 (see comment 18).
To summarise, you basically need to uninstall overlay-scrollbar and liboverlay-scrollbar-0.1-0.
This can be achieved either using the package manager or aptitude
sudo aptitude remove overlay-scrollbar liboverlay-scrollbar-0.1-0
This has the added benefit of removing the annoying scrollbars that come with Natty.