It all began after launch when a huge number of people experienced the dreaded stuttering when moving the camera during gameplay. This was an unusual problem because it tends to happen when framerate is apparently maxed out at 60 FPS. There are too many threads on this for me to link to, but it's now accepted to be due to the engine maxing out at 64 fps like some past Bethesda games. The extra frames are causing the stutters. There were 2 generally accepted "solutions" that people discovered:
1) Turn Vsync off
2) Use a framerate limiter
There are issues with both "solutions". By turning Vsync off, you allow the framerate to go above 60 FPS at times, and the result was physics glitches (where things would fly around violently upon contact), and also graphical glitches where black or grey bars would flash across the screen rapidly. The second "solution" was mainly in response to the first "solution". People began capping their framerates using Dxtory or Skyrim antilag, myself included. It was only through conincidence that I noticed that these limiters also resulted in engine issues:
http://www.gamesas.com/topic/1275049-arrow-delay-glitch/
http://www.gamesas.com/topic/1321635-delayed-actions/
http://www.gamesas.com/topic/1327300-arrow-lag-after-shooting/
Basically, capping the framerate to anything at all would result in timing desync in the game. Symptoms include arrows shooting many seconds after release, menu loading delays, and recently confirmed cell loading issues:
http://www.gamesas.com/topic/1337843-14-does-not-like-dxtory
I've personally experienced majorly delayed cell loading ONLY while using a framerate limiter, so this definately wasn't an issue tied to 1.4 beta as that thread suggest. I've also noticed that I no longer CTD at all after removing my framerate limiter.
So now it's all clear why Bethesda shipped the game with no V-sync options - the game must run at 60 FPS maximum or you would get yourself into all sorts of issues. This basically means the only way to play the game is at a default 60Hz as imposed by Bethesda. To support this claim, here's a sample of other issues that arise when your monitor(!) is not the default 60Hz:
http://www.gamesas.com/topic/1329030-bug-annoying-sound-something-stuck-sound-in-inns-and-shops
http://www.gamesas.com/topic/1338894-running-skyrim-with-120hz-monitors/
http://www.gamesas.com/topic/1338218-skyrim-long-load-times-on-1080p-24hz-bug
I think it's pretty clear that Bethesda made a MAJOR mistake tying the game engine not just to framerate, but the REFRESH RATE of your display. Sure, I'm hoping that Bethesda respond to this in some way so we will now if a fix is coming or not. I don't have my hopes up because it seems like the foundation of the engine was built like this, and correcting it may be an unfeasibly big task.
Please post any experiences you've had that support my findings (or refute them!), so that this thread can educate people experiencing these issues and hopefully stir Bethesda to action.

until problems are fixed by Beth, it's down to people like us