Thank you for this bugs list and the time you've taken to compile it. It is a great reference point and sanity calmer to know that others have recognized the problems and therefore maybe (or have already been) dealt with. I,ve experienced many mentioned in this topic myself.
May I mention a few things I did not notice yet in the list:
Quest Items
In Markarth, The Reach, If you kill Lisbet (The Canibal) of Arnlief and sons Trading Company and loot her inventory after you find her statue of Dibella, the statue will become stuck in your inventory (as it remains a quest item.) Serves me right I suppose.
Graphical Errors
The forge graphical glitch you mentioned with DE Female seems to be random. I made 2 Breton chars. The first one pummelled his metal correctly while the second char (same race, six but different preset fetures) didn't always know which end was the hot part

Possible Workaround: I went to the Skyforge to make stuff and it never seems to glitch plus it seems to set the glitch right for a while at other forges. (But eventually returns)
Dragon Glitches
I noticed you said the glitch at Dragon Tooth Crater was fixed after patch 3.1 however I still come up against an indistructable dragon (post patch) that crashes into the ground in front of the word wall with it's head burried in the ground and it's legs and tail stuck in the air, thrashing wildly)
Solitude House (Proudspire Manor)
If you purchase the alchamy upgrade for your house, it will replace the very useful cupboard and any items you stored there with an alchamy table! So buyers beware! I think it is the only house upgrade that actually removes containers from your house? Make sure you remove all items from that cupboard first!
More Dialogue sticking?
Helgird of the Windhelm Hall of the dead will have a morbid fascination about the wounds of the murdered Susanna the wicked. In her cript or wandering the streets she will comment on the long slash made on her body if you greet her for ever afterwards and sometimes as a passing comment too!
Dead things rising!!!
Sometimes if I kill a creature or person it will stand right back up as if alive, moving and sometimes making noises. It will not attack and you cannot kill it with weapons or interact with it in any way. Annoying if there is an important item on it. However I have found a workaround. If it is not too powerfull, you can hit it with a raise dead spell and it will start to glow like a thrall and eventually turn to dust and it's inventory can be accessed. This usually happens when I use a dagger I enchanted with soul trap and fire spell. Why? I don't know...
Some of these things are a bit picky, I know, but there you have it.
Items placed in player owned house
Just as a possible quick fix to this problem already mentioned in the list on page 1. If you place your items in your house (as long as it's on a stable surface and save your game (you don't have to exit the game, just save) it seems to make the game fix the items in place -until you interact with them again, of course. I have done this after much experimentation and getting annoyed at the game rearranging my dropped items. For me it seems to work. I hope it does for you too!