An inventory category for quest items would be nice, I wouldn't even mind stuck quest objects if that were the case. Especially since quest items are weightless.
In the case of the Giant's Toes, though, that's just something that shouldn't happen. If you've got 40 toes and one of them is needed for a quest, you should be able to do whatever you like with the other 39. I prefer them with a little Nord Mead, myself.