I'm looking for a plugin that will be able to disable other plugins per world. For example, I only want factions to work in a single world. If this is possible, and someone could make it or lead me towards a plugin that does so, that would be great. Thanks.
You can do this with most any Permissions plugin. Just add the permissions for Factions to the desired world.
same thing, if you block the commands then there will be no factions in that world. That is about the extent of Bukkit, they don't have a way to run different plugins on different worlds. If you want it, then you must ask EACH developer of EVERY plugin to add in some type of multiworld support.