I have a ladder with a teleport from the top to bottom, but I seem to remember always hearing this was a bad idea. What's the verdict on a teleport like this within the same cell? OK to do or bad idea to do? I seem to remember that it would mess up your quest pointer or something.

I think, the only thing it messes up is the quest marker, for reference see the Greybeards' little tower in their courtyard.

Ive never heard of anything wrong with doing that. Ive done it many times with no ill effects, plus it is done in vanilla in several instances.