I have seen that there is a dedicated Dojo component for handling Flash content: dojox.av.flash - I suppose it is intended solely for the purpose of adding Flash .swf files into the Dojo content ...
But what about adding content for plugins other than Flash ? E.g. for a plugin that can serve 3D content ? Is there a dedicated component meant to be used as a starting point for such a use case ?
What are the rules for having 3rd party plugin content playing together well with Dojo on the SAME webpage ? Which Dojo components can actually deal with 3rd party plugin content - e.g.: Can it be layout managed by Dojo somehow ?

It depends on what the plugin allows.
Including a plugin and working with it is pretty much a straight-up standard thing; you can simply work with one the same way you would with straight-up JS. We wrote the Flash and Quicktime ones (which have been moved to dojox.embed) because of some version detection things, and because of more advanced work we will be eventually doing with both of those mediums.
If there is a specific plugin you're looking for help with, you should post more info about it and we'll see what we can do.