At that moment, I smelled it, the "magic smoke", I may have touched that 5v connector with the PCI slot cover, being metal - and it was earthed to the case because it was still connected to it, you know the cheap cases that force you to remove these covers by breaking them out

Well, it was very acrid this smell, no smoke was actually visible, but this was that distinctive smell that comes from burning out small components on PCB's
I immediately switched the power off when it happened, rebooted and the PC boots......
I removed the board for inspection, no visual damage on either side of the board and I can't tell where the smell came from, it's not the PSU or graphics card or anything else, the smell was strongest over the PCI slots, no longer evident.
I'm not sure what to do next, I'm not even sure I shorted the 5v pin on the SPDIF connector, but it seems very likely.
This was a spare PC of mine that I've just spent days on, preparing it for online gaming for an associate
