My game micro-stutters at 60 fps only when indoors. This happens in all interior environments, dungeons, houses etc. I still pull 60 fps when it does this so it's not a frame-rate issue. What I mean by micro-stuttering is shown perfectly in this video of BF3. It looks exactly like this.

http://www.youtube.com/watch?v=MMPFfjupeq8

Is this a common issue, and is there a fix for it?

System Specs
i5 2300
7870 OC Edition
8 gigs ram
1920x1080 resolution, playing Skyrim on Ultra with full AA and AF.

IIRC this is known issue with the games engine and refresh rates. The recommended advice as far as I am aware is to use a frame capper program to not hit 60fps where the bug occurs. Limit the game to 50 or 55 and you should be good to go.

I disabled V-Sync and it made the issue a lot better, it hasn't completely gone away but I'm well over 100 fps everywhere now so I don't think I will be hitting 60 often. However, now I get the occasional tearing that results in not using V-Sync, so I will take you up on the advice. What frame capper do you recommend?

Disabling V-Sync has other side effects, as well. The game itself assumes V-Sync for things like physics. So you can have anomalies in more ways than just visual.

Nobody knows what the best software is to limit fps? MSI afterburner comes with a bunch of stuff I don't want to use and I don't think I can disable that. Is Dxtory a good program?

Your best bet with ATi would be MSI Afterburner, it may seem confusing at first but your learn to love it.

Can't comment on Dxtory, never used it.

Ive heard good things about Afterburner, never used it myself though but its been recommended to me many times. Never heard of Dxtory, sorry.