Right in case anyone ever runs into this problem, I tried nearly everything even calling the local Apple dealer to try and sort this without a re-install.
Turns out this issue must have been caused by plugging in my external 120Gb hard drive as I went to a mates house and plugged in my HDD to his G5 running tiger and guess what. His Main drive vanished as well!
So, after much searching he managed to come across a fix for this issue.
Launch ScriptEditor and copy and paste this into the script window:
tell application "System Events"
set visible of disk "NameofDisk" to true
end tell
tell application "Finder" to quit
delay 1
tell application "Finder" to launch
Replace NameofDisk with the actual name of your disk, hit the Compile icon to make sure the script didn't acquire any errors, and then hit run. This should set the visible attribute back to visible and quit and relaunch the Finder, thus making the change available.
The same thing can happen to other drives, both internal and external. You can use the same Applescript to fix those as well, just put in the name of the drive.

Now my drive is now visible again without a full re-install, this works for Tiger and Leopard too!
Hope this helps someone who runs into the same problem in the future.