I use a lot of methods when the stem is just a bit crudy from my smoking it, including Mr. Clean magic eraser sponge, Barkeepers Friend cleaner, etc. However, when I get an estate with a really badly oxidized vulcanite stem, the only method that really seems to get it back to new looking is sandpaper. I start with 400 grit and work my up to 1600 or 2000 grit depending on how nice a pipe it is and how much work I want to put into it. I use the black silicone carbide paper, keep it wet with water and rinse it often (both paper and stem). I get the oxidation off with the 400 grit, then work through the rest of the grits (I think I usually go 400, 600, 1200, 1600) to polish it to a nice shine.
I always finish up with a pure carnuba wax on my wheel, even when just doing an after-smoking cleaning I always wax as the last step.
You do have to be careful with sandpaper not to round off any sharp edges or create any sharp edges that are not supposed to be there. You can also clean up shallow tooth marks, shape the button, etc but depending on the stem you may or may not have a lot of material to work with. Practice on a cheapo before you tackle a Dunny!