Hey stunts, I am having EXACTLY the same problem with Dolphin that you are. Just like you said every 30 seconds or so the gameplay slows way down to an unbearable speed (like maybe 6 fps) and then it just comes right out of it and goes back to full speed. It doesn't seem to matter what game either. Back when FF4-TAY came out I set up Dolphin and had played about 10 hours into the game with no problems until my crappy AS-Rock mobo died on me. I finally got a new ASUS P5KPL-CM and also upgraded the video card to a 7900 GS (from a 6800 XT) and that is when this problem started. I haven't messed with any bios settings or hyperthreading or anything like that yet, but I did try several different versions of dolphin and messed with all kinds of settings - all of which had no effect. I play games through steam all the time and right now I am playing Bioshock and I never have any problems. Attached is an Everest hardware specifications report (HTML format), if you want you can compare specs. Maybe that will help to narrow it down because it seems this could very well be hardware related.
Edit 12/03/09
Well I fixed the problem. While playing Bioshock I noticed that I was getting some audio distortion, so I updated my sound drivers - which did nothing. Then I decided to try my old SB 128 that I have from years back and Bioshock sounded great after that. Thought maybe I should see if that affected Dolphin and sure enough the problem is gone. Maybe try either updating or downgrading your sound drivers?
Edit 12/03/09
Well I fixed the problem. While playing Bioshock I noticed that I was getting some audio distortion, so I updated my sound drivers - which did nothing. Then I decided to try my old SB 128 that I have from years back and Bioshock sounded great after that. Thought maybe I should see if that affected Dolphin and sure enough the problem is gone. Maybe try either updating or downgrading your sound drivers?