My computer is suffering of slow-downs and I'm not surprised (it's around 6 years old). Here's what I've verified:

1. They are not very frequent (only a couple of times a day).
2. When they happen a single application will hang for 10-60 seconds, while the rest don't hang but also get slow.
3. Even as it is happening, the CPU usage stays low.
4. It happens to applications (such as text editor, firefox, skype).
5. It never happens to some applications (such as games) which I use for hours under heavy CPU load.

Also of note:

1. The Graphics card and PSU are new (around a year).
2. Though I have a decent amount of software installed right now, this was happening even right after I reinstalled Windows.
3. This HDD has been through many partinioning schemes, and a few heavy operations (such as moving around 200GB of data).

Because of the above, I am already 70% sure the problem is with the hard drive. Before I replace it, however, I want to rule out other less likely possibilities (such as RAM, software, or PSU).

I don't have the money to replace the entire box right now, but I can easily replace one of the components.

I've read several questions (such as this one) which give general guidance on troubleshooting an unknown issue, that is not what I'm looking for here.

My main question is:
What tests or benchmarks can I run to verify I have a problematic hard drive?
I don't need to solve this problem, I am content with just making sure it's the hard drive.

I could borrow a newer hard drive from a friend and see if it gets better. A positive result would rule out all other components, but it wouldn't rule out a software issue (since this new hard drive won't have any of the software I use daily).

Running on Windows/Linux.