I would advise that you do not join the meshes after you create the gums and teeth. Really there is no need as geometry-wise they do not need to be joined. Grouping them would work, one of the points of grouping is for organizational purposes. Keeping them as separate objects is always a good idea unless you need to make them one object for a specific reason, as it is easier to change your work without having to detach the objects again (I've had to do it before, it's a pain in the ass.)
I just realized you probably mean as actual separate objects instead of separate meshes. In that case, I may almost recommend the same thing. It would be easier skinning the model if you kept the teeth as a separate object. On the other hand they could also work as a good reference for creating morph targets with the mouth (you don't need any morph targets for the teeth/gums). So you could simply use them as a reference then delete them in the end and have the two halves of the mouth as separate objects. Or, if you plan to morph all of the facial movements, it would be best to keep it all as one object.
Really in the long run I would say it all depends on the situation and what you plan to do with the model.
