Please read this for more info !
First, I'm french so I apologize if my english is bad ^^
I managed to tweak Dolphin 3.0 rev 201 so MGS cutscenes run smoother than in my last attempt. Still some graphical glitches and crackling sound though, but best quality so far. Recorded with FRAPS and edited in VirtualDub.NTSC version of the game used for it runs better than the PAL version. Settings used for the game can be found here : img207.imageshack.us/img207/49...
vBeam emulation unchecked so real-life footage can be displayed properly and help cutscenes to run smoother, but may cause audio async if cutcenes run faster than audio. It happened to me from when Snake and Baker begin to talk after fighting Ocelot, so you wanna mess with internal resolution and SSAA to slow the cutscenes and avoid async (it depends on your hardware, you may have to try several configurations before finding a good one for you that allow you to have both smooth gameplay and cutscenes). You can check VBeam if you don't care about real-life footage and having a few cutscenes less smooth, however you may still have a little async (like 0.5 sec).
No framelit cause setting it on auto or 60 fps messes the sound a little, causing ultra short drops every 2 seconds, which is very annoying once noticed. So be sure Enable Audio Throttle is checked, otherwise sound will rape your ears.
Checking DSP LLE recompiler will provide you best sound. HLE emulation is buggy with this game, you might notice annoying sound peaks, and sometimes audio cuts that will lead to unprevented Dolphin closing.
Please ask your questions in comments if you have, I'll answer you the best I can (only about this game of course)
My PC specs : I7 2600k oc@ 4.4ghz, Nvidia GTX 570, 8 gb RAM DDR3, Win7 Pro.