I recently installed Eclipse Indigo. I wanted to add a few plugins to it, so I tried to use the UI to check for new updates and install some new packages. I let it run for a while, and after about 45 minutes, it looked to be about 20% done. Eventually, it displayed a few errors about timing out.
The issue is that Eclipse appears to be trying to contact mirrors that don't have a proper copy of all the files it's expecting. My solution was to invoke eclipse with the following flag. Add it after "eclipse", or in eclipse.ini