OK. I fixed the problem, for me at least. My time capsule wasn't even showing a light on for the ethernet port, the card in my mac pro was clearly powered down which would explain why the magic packets go missing.
10.6.8 contained a modified version of /System/Library/Extensions/IONetworkingFamily.kext, more specifically /System/Library/Extensions/IONetworkingFamily.kext/Contents/PlugIns/Intel82574L. kext.
I replaced IONetworkingFamily.kext with the version that was present before the 10.6.8 update and my WOL now works once more.
So I'm pretty sure right now that 10.6.8 broke my WOL and I'm also pretty sure I fixed it but I'm not sure what other issues I'm causing as a result.
I have no idea how I get a reaction from Apple given that I have no "support credit" but surely they should support a customer with regressed software. Anyone got any ideas?