I install Eclipse from the Software Center so it links up and will be updated with the rest of my software. Because I am developing for Android, however, I have to install the ADT Plugin within Eclipse by going to Help > Install new software (or something to that effect). Now, I do understand that I can update Eclipse through the actual Ubuntu software center/system, but in order to update plugins and extensions within Eclipse, I have to go to Help > Check for Updates (which then scans all plugins for updates). The only issue, is that when I installed through the software center, the owner became root, and whenever I run it without root, I'm not able to update - I get the error message "Insufficient access privileges to apply this update." When I run it as root, all of my plugins disappear, because I guess I installed them as myself, not as root. I tried to install the plugins as root, but the Install New Software choice would not work.
Ubuntu 12.04 and Eclipse 3.7.2-1