What a morning - spent approx 4 hours called my machine all sorts of foo'in names, but finally all is well.
This is my experience, am hoping this post will be cathartic...

It began quite simply but the arrival of a new hard drive. I have 2 in my system, and wanted one external, but i decided to move the new one into my system and move the smaller of the 3 (160GB), previously a media drive (not windows) to become the new external. All seemed well.
Opened up the PC, hooked up the drives, copied stuff across, swapped them out, and all ready.
Booted to windows.
No audio.
Strange. But i'd occasionally had probs with my Audigy 2 card before that simply rectified themselves, so a reboot.
Hung on the Windows XP load-up screen.
Slightly bothered. Reboot.
Hung again. x5.
Then no visuals at all.
Not happy at all.

Dug out an old PCI video card, slung it in, cleared the CMOS, and managed to get video over PCI -> Analogue, into the BIOS, all was set well, very strange.
Booted to windows, no PCI-express card in display drivers, no Audigy card.
Very concerned at this point.

I spent the next 3 hours with all sorts of BIOS flashing (up and down), changing PCI slots, getting on the verge of buying a new replacement 939 motherboard (which would pi$s me off as I really want to go Core2Duo at some point but cant afford now).
Tearing my hair out, sweating, shouting, not a fun person to be around.

And then a flash of inspiration.
I got some sterile alcohol wipes, and cleaned to connectors on my motherboard and on the cards, thinking "what the hell".
Booted up and suddenly ALL IS WELL
Audigy present, video working over PCI-express!

I can't tell you how relieved I am, and hope that this post might help someone else in a similar situation. It's still a crappy buggy motherboard that needs replacing, but all the sweeter when I get a Core2Duo system.