Experiencing slow-downs, software issue?

In the last month I have been experiencing slow-downs in all the applications I have installed, Safari, VLC and so on.

For example, when I´m watching a movie in VLC the movie stops for about one or two seconds, two or three times every 10 (or so) minutes throughout the movie. This happens regardless of what i´m watching, 720p, 1080p, or low quality podcasts.

Safari just stops, showing the beach-ball in two or three seconds.

Finder can use two or three seconds opening a folder etc.

The CPU stays cool, and stays at the same percentage of use when this happens.

Does this sound like a HW-issue? It seems like its the HDD, so I did a test, but "It seems to be okay", thats what the disc-utility states.