Jesper,
Eclipse M6 core has a known memory leak problem: https://bugs.eclipse.org/bugs/show_bug.cgi?id=402912
If eclipse is used for a while it will run out of memory because of a leak in the saving of workspace state.
Any chance that is what you are seeing ?
They will fix this in M7, but until then the following is the workaround:
"The workaround for M6 is to set the Preferences>General>"Workbench save interval" to 0, which disables it."
Does that help you or is it something else ?