If it's low pitched, it's usually mains hum if the Ext HDD is mains powered. If that's the case, it might be a dodgy earth connection - if not, a prob with capacitors. If the Ext HDD is USB powered, then I've no idea!
Could be re-siting your speakers has caused electromagnetic interference from close proximity to the PC case.
You could try moving the speakers about to see if the hum becomes less or even worse.
If the hum is a harsh (what I used to think was mains hum), it might be a faulty connection between the speakers and the green 3.5 mm jack plug for the socket coloured green on the back of the PC. - try a replacement lead
My son had this problem, and it turned out to be as simple as the fact that the speaker cable was running at some points right alongside a power cable. Moving the speaker cable fixed it. Like onthelimit suggested, it sounds :-) like earth hum.