I understand it is way too early for implementing anything of this kind, but I'll start venting the idea, so that it does not fall through...
A plug-in manager would be nice to have, tentatively with the following basic functions:
*) list of all installed plug-ins, possibly with title, version and contact URL / e-mail of the author
*) choice to enable / disable each plug-in (without actually uninstalling it)
In single-player, it could be an option in the top menu (parallel to "Single Player" / "Multiplayer" / ... options) or of the "Settings" dialogue box(es). I believe the requirement to be out of any world in order to change the status of a plug-in would be perfectly acceptable.
With a dedicated server it would be probably more complex, but a way to enable / disable individual plug-ins without restarting the server would be great.
P.S.: I think it is better to keep this purely local functions separate from other functions which would access external resources, like a plug-in downloader/installer. To discuss the latter, it would be better to open a separate thread.