Windows Video stuttering after some playtime (DVD folder)

Have you experimented with the "sync playback to display" settings?

Haven't done that yet, since I thought this would only be a good option if the display has a fixed framerate and adjusting the display to fit the framerate of the movie would be the way to go to get a perfect playback. My TV has no problems with displaying those framerates, if I play those movies from the PS3 playback is super smooth.

But I'll give it a try, is there any particular configuration that I should start with?

I think you are right about that. Unfortunately my TV doesn't tell me the frame-rate it is running at, so I've never really got to test this out fully. It may do nothing for you, but I figure it is worth a shot. The only time I see some slight studdering is when watching Swamp People on the long panning shots, and I think that has more to do with the files themselves than XBMC's playback.

So, for now it seems I did find a working solution. I activated "sync playback to screen" with the audio resample option. With that the occasional framedrops in HD content was gone and I did not came across any microstuttering in SD content. After a while i realised that some files (HD and SD) just start to drop frames every 10 seconds, I then deactivated deinterlacing and everything was smooth. I didn't come across any flaws in playback with that setup for some time now, so hopefully this is the solution.
Just wanted to share, in case someone is experiencing similar playback problems.