I tried all kinds of things to solve this issue and gave up and continued playing. Then I suddently noticed a pattern to the stuttering; when there is a lot of light in certain areas, like candles or torches and even magic or just fire...

I went to Nvidia control panel (Don't think ATI Cards can force this on) And turned off Ambient Occlusion (which I had on quality) & micro stuttering was gone in indoor areas & massively reduced in outdoor areas...

I don't know whether this is a problem with my nvidia driver (290.53 beta) or my Graphics Card (Asus 560 ti 1GB) not working well with the driver and or ambient occlusion, but turning it off was beneficial for getting fid of my micro-stuttering.

Hope Nvidia notice this & fix it for the next WHQL release, or Bethesda if its there current patch not working well with the Nvidia beta driver.

Thanks for reading.

I find the areas that tax my graphics card the most are the underground caves with lots of blue hazy ice everywhere

there's some weird stuttering on AMD cards too.

i had to disable skyrim's crappy internal vsync (ipresentintervalsomething) and force vsync through AMD's catalyst control center -> stuttering was gone.

the only places i get stuttering regardless of what i do... and only in specific places where there is usually a ridiculous amount of mist/fog or something.. mostly in caves/dungeons...otherwise i get none at all.

The door to exit Warmaidens in Whiterun is really bad for first person stutter. Dxtory @ 59fps locked fixed it for me. Not sure If I've suffered any ill effects because of that though.

the people with fog stuttering may want to try this mod

http://www.skyrimnexus.com/downloads/file.php?id=736

i'm a fan of the fog though.... so i live with it.. i just think the reason i'm having issues is the way they implemented the fog/weather effect... plus running at a high resolution doesn't help those conditions.

whats a microstuttering? i only know this term in relation to SLI/CF systems. How many fps Fraps is actually showing? Bad felt fps can also be caused by jerky mouse movements. There are tweaks for that, but im too lazy to searsh, since if you have vsync on and are dropping to 20fps that would be the source of the problem.

Micro-Stuttering is basically a continual stutter, but a much more subtle than what you would call a normal 'Stutter' and microstuttering doesn't really affect FPS, its just as annoying lol - for a better & complex explanation, view: http://en.wikipedia.org/wiki/Micro_stuttering & the best videos I could come up with was this: http://www.youtube.com/watch?v=zb3MsENJ-fU&feature=relatedhttp://www.youtube.com/watch?v=zOtre2f4qZs and
This: http://www.youtube.com/watch?v=MMPFfjupeq8 - This battlefield 3 vid is good as it has a real bad case of micro-stuttering similar to the degree I was experiencing with Skyrim - But as I mentioned, when I turned off Ambient Occlusion, I now only have it outdoors in cities & not as much as before (indoors & outside of cities, no microstuttering at all) - hope this helps.

Stuttering can be caused by a lot of things, including things you cannot control, like driver bugs and game issues AO is taxing anyway.

Thats all very interesting, but you dont have a multiGPU system, taken from the first port. So download www.fraps.com , and check fps. It looks like you just havent disabled vsync, which is automatically forced by Skyrim. Which does all the described things. More specifically if your PC cant maintain 60fps, it will jump directly to 30fps, which is perceived as stuttering, which it also is. Logically when you decreased video quality, or are playing indoors, fps improved. no more stuttering.

Edit: Open C:\Users\XXX\Documents\My Games\Skyrim\Skyrim.ini add or change under [Display] iPresentInterval=0

I did try all that, but to no avail. When I disabled V-sync, the stuttering was still present to the degree it was before and my FPS are always around 40-50 (25 at Markarth lol) - I am using a couple of ini tweaks like bTreesReceiveShadows=1 for more realism and fSkyCellRefFadeDistance=100000.0000 so that my distant view is more detailed.

I find my system coping with Skyrim generally good as a whole - I am not an expert on stuttering and may have overlooked something, but I spend the good part of maybe 3-4 hours trying different combinations of Nvidia Control Panel adjustments and Skyrim settings + ini Tweaks - the only thing that worked for me was turning off AO - go figure lol

Anyways, if anyone else has a stutter or micro-stutter fix, let us know - here is my whole system for comparison:

Processor - Core 2 Quad Q9550 E0 (stock)
RAM - 4GB DDR2 800MHZ (stock)
GPU - Asus 560 TI 1GB (stock)
Mobo - Asus P45 P5QSE
PSU - Corsair TX 650
Case - Antec Nine Hundred 2
Sound - Sound Blaster Silencer Arena 5.1 Surround Creative Headphones
Nvidia Driver 290.53 Beta
Resolution - 1680 x 1050 (22'' Samsung T220)

Skyrim Settings:
All On High (not Ultra)
View Distances / Fade: On Max
Antialiasing: x4
Anisotropic Filtering: x16 (Nvidia - looks better)

Extas:
Using D3DOverider For Triple Buffering
Using Skyboost

This. I've got it locked 30 fps and stuttering is greatly reduced, but general engine stuttering remains.

THIS... this just started happening to me 3 days ago. And it happens MOSTLY with only one of my three characters that is a destruction mage who's favorite spells are FLAME and FIREBALL. When those are in the ready I get what I thought was not micro-stutter but perhaps it is. When I cast them (holding down the buttons for flame) I generally get more stutter. if "put my hands away" or change to other spells the problem will stop.

I never realized that for me, the flame was mostly the problem until I noticed it happened on my Figther but primarily only when carrying a torch, and mostly even then, only when drawing or putting away his weapon. It sometimes happened around the fiery cisterns I noticed too.

I'll try the Ambient Occlusion fix. What's odd is this JUST started happening 3 days ago for me, and I've not had any changes to .ini files, drivers, etc,. on my system.

Edit: Nope. No help. But I did notice something. Lately my shadowing on grass and textures hasn't looked up to par. I noticed in Nvidia Inspector that the Ambient Occlusion compatibility was set to Skyrim (I used to have it set to Fallout 3 per other recommendations and before the beta update drivers). I changed it back to Fallout 3 compatibility and the shadowing looks MUCH better to me.

Same here on my rig also sometimes around fire and smoke but its not as much and none of my issues seem to be as annoying as yours but it is noticeable. Probably the only areas where the game even taxes my GPU and CPU at all.

Well. I just fixed MY micro stuttering issue after trying FPS limiters, Disabling Ambient Occlusion, and all other manner of tweeks. One thing I did change on my system is I recently installed a Color Munki for monitor calibration for photography work. This created a new ICS profile for calibration which it dynamically updates. I had uninstalled the software and that didn't have any impact, but I went in and CHANGED the color profile back to the original Windows 7 color profile and THAT fixed the issue for me.

I had stuttering then I plugged the computer cable directly into the wall socket instead of an adapter with 6 other things in it. No more stuttering.