Disk I/O Errors – How to Pinpoint the Cause

I am getting (seemingly random) disk I/O errors on my bootdrive. At first I thought it was caused by a faulty hard drive, but now I've replaced it and I still get those errors.

These are the steps I have followed beginning from the first time I noticed something was wrong:

1. Laptop hangs with just Google Chrome and Postbox (an e-mail application)
2. I restart the laptop, but it never gets past the screen with the grey apple.
3. Started Apple Hardware Test by holding "D" during startup. This came up with no errors
4. Through Verbose mode, and Disk Utility of the install CD I saw that it had disk I/O errors.
5. I switched the Momentus XT drive for the stock Apple HDD.
6. Installed a fresh copy of Snow Leopard
7. Recovered everything from a Time Machine backup

After a day it started giving disk I/O errors again in Console.
This makes me think that an app or a setting is causing this as it is unlikely that both the hard drives are corrupted.

How can I pinpoint which application is the cause?

Below are my system details:

MacBook Pro 5,3
2.66 Ghz / 8GB RAM
Snow Leopard 10.6.8
First HDD: Seagate Momentus XT 500GB
Second HDD: Stock Apple Hitachi 320GB