I would like to settle on a tool to create/maintain my custom eclipse distrib (starting with next 3.6). By studying previous questions main contenders seem:
Same plugins: I would just create update site with my plugins, or composite update site pointing to update sites with plugins you're interested in. Or you can simply use Eclipse Marketplace, which can create such update site for you from plugins you mark as favorite. Yoxos and Pulse should also work fine.
Same settings / preferences: Workspace Mechanic from Google may do the job for you. Beware: it is new project, which was just released into public. Disclaimer: I have no real experience with it :-) Pulse Team Edition should also be able to help (see previous disclaimer though).