Word of warning - apparently not all the places you store stuff are safe.
I put a bunch of crap (including my full set of Nightengale armor) in one of the barrels by the blacksmith in Riften - I don't know if it had anything to do with loading the latest patch, but when I went back to check the inventory, the barrel was empty. Not that big of a deal since I'm level 52 now, but annoying nonetheless.
Also, that glitch with the companion quest has still not resolved itself. I'm getting the impression that at some base level the game just blew a gasket when I cleared that particular dungeon early, and even though I went back to an earlier save point, it is just ****ed up and that's the end of it. The people in Whiterun are still standing around like morons even after I moved the bodies. The most annoying thing is that I'm stuck with the werewolf thing now, which I never use and which also prevents me from getting the rest bonuses. It may also prevent the marriage quest, since putting on the amulet does nothing when it should spark interest in certain characters.