HDD Lagg...Pls help!

I was writing about 20lines to explain my issue but then my IE crashed, lol so i'll write shrot and brief this time.

Problem : HDD Lags. when no specific softwares running.

Things I did :

1.Checked the process and found no problem or programmes that could cause lag.
2. Checked for virus/spywares.
2.5 Checked the HDD using Manufacturer's Disk Analysis Tools (Extended test)
3. Tried the full format of the HDD.
4. Tried installing different HDD.
5. Tried different brand of HDD.

And after all those, it still lags after a couple of hours after new windows installation. (the hours varies)

Soemtimes it takes 3-5minutes to load a single IE windows imagine that..

Still, once it loads, such as games, it plays fine most of the time. (not all)

So here are my guesses for cause of this problem.

-Faulty RAM
-Faulty Motherboard /or HDD controller
-Faulty Power(? unlikely aye?)
-Windows. (? maybe? unlikely?)

Do you know if any of those above could cause the problem I have?

Pls help! >_<