Right, update:
Gromited the PSU fan and no difference, so I decided as a few said on here that it must be the HDD's, so I made some silicone feet (using sealant) and tried again. Lo and behold the humming had gone and the machine was very silent. However I couldn't get any signal to the monitor...
After a week of non use I managed to go out and get a DVI-VGA adaptor thinking I may have broken the old one, nothing happened, so I swapped the PSU cables around in the PSU (modular) and signal worked (I fiddled with some other stuff as well so maybe...).
Anyway after using it for a day I realised my newest 500GB Hitachi HDD was missing, with all my media on... So out comes the PC AGAIN and I find the power cable has been knocked out, plug it back in and turn on again, humming starts again, with vibration of the case going from practically nothing to noticeable..
I've just unplugged the power cable again and the humming has gone again, so it's obviously just that HDD that is causing the problem. Which to me indicates maybe a dud HDD? It still seems to work and there is no *click of death* however none of my other (older) Hitachis' hum up and down.
RMA? It's only about a year old.