What programs do I need to find the problem

So I bought a laptop and it was working well (however had some problems with streaming audio or audio stuttering in games) but the other day it just became really really really slow, 25 minutes start up time, opening a folder would take one minute and to do anything like opening stuff programs would cause the computer to halt for about 30 minutes.

So instead of trying to fix it by trial and error (with the slowness of the machine it could take a week). I decided to format all drives and reinstall windows, my usual quick fix, but alas to little avail.

The system is faster but there is still a delay happening and the windows start up is between 10-15 minutes, so I updated all drivers but the problem persists.

Anyway in short, this is my question, what programs should I use to isolate the problem. I have HD Tune running now (and the results are not looking good, its jumping from 0.1mbs to 50 mbs erratically).

Is there any other diagnostics tools I need to be running.

My specs are :
Intel HM55
Core i5 480m
4GB Ram (Not sure which brands, but two sticks of different brands)
ATI HD5700 1GB
Toshiba MK5065 GSX (500gb)
Windows 7 Ultimate

Cheers guys,

I think HD Tune comes with a disk scan, run it. Don't bother with the Windows checkdisk, you need to run a low level drive test. The BIOS may have a drive test also.