I am running the Steam version of Skyrim on ultra using an i5-2500k and a HD6950 unlocked. The game plays smoothly between 45 - 60 fps.
The thing is that even when I maintain a constant 60 fps in certain areas, there is micro-stuttering or frame skipping issue, which is noticable
every now and then. I guess this is the same problem existing in all gamebryo games. It really made me sad since I am very sensitive
to these sort of frame rate problems.

After trying endless number of tweaks with .ini files, the issue persisted. What solved my problem is the following :

I run the game in windowed mode and use a mod which removes the borders. So, it practically looks the same as full-screen.
The mod can be downloaded from : http://www.skyrimnexus.com/downloads/file.php?id=4

I dont know whether this might prove useful for any of you guys but it solved my problem and the game runs without any micro-stuttering now.

I've noticed very slight microstutters but to be honest it's a vast, vast improvement over Bethesda's previous stuff, it took several user made hacks to solve the 64hz/stutter issues with Oblivion and Fallout 3, you're not wrong though, vsync is not immaculately smooth but it's within my tolerance levels now.

Fixes first person microstutter! Border-less windowed mode! Requires an advanced graphic tool like RadeonPro with high API detection in order to force V-sync to work.