Since your specs are similar to my mines. Have you tried changing power settings to high performance? Try lower full screen resolutions and anti-aliasing on your games.
Yupp, tried that.
I just rewatched the video, and I noticed both your CPU and your GPU usage is a bit "low" (maybe not for Minecraft, but still...).
Go into your BIOS, see if there are any power save options enabled. These could restrict CPU/GPU performance and give you that stuttering.
EDIT: oh, and run a SMART check on your HDD if you think its bad.
It always does a auto SMART check on every start-up and I took one in the HDTune program. The only thing it complaining about were some relocated sectors or something :S Was 10 of them.
And it happends to EVERY game. Even on Terraria when I die it drops the FPS. I made a post on reddit and one guy made me do a latency check when I was still on W7. Heres the result: