These are my ideas. I have no technical background so I'll accept any technical corrections.
If we are to abandon x86 I'd suggest to reconsider the entire electricity household on the motherboards and work with higher voltages and lower currents. There is a reason why transport of electricity is done at extremely high voltages. Also work with one voltage only (48V AC balanced or so), not 3 at various polarities. This should make it easier to manufacture a quality PSU. The balanced power will kick out 99,999% of hum and noise. (not fan noise).
Integrate shielding in the motherboard so the interference with my soundcards is kept to an absolute minimum.
Bigger RAM-chips so we can have 8, 16, 32GB etc RAM-sticks. You should be able to decide yourself how much of your RAM is non volatile, so RAM sockets will need to change too.
Ditch PCI in favour of PCI-E and make the width user configurable i.e. I can decide how many lanes I dedicate to my video card and how many to my soundcard. If I have a hefty professional soundcard (RME, MOTU etc. not Creative), it will of course get a lot of width. In the future we might need more than 16 lanes, also in order to put every other i/o protocol on the PCI-E bus: USB, FireWire, LAN etc. As earlier suggested, maybe we can look into unifying those into one standard. Ditch all legacy ports for sure especially if you ditch x86.
HDD's can still be useful but not for streaming and working on data, just for storage. With 16-128GB of RAM you should be able to put your entire project into RAM and work on it from there, only save when you think it's necessary.
And for crying out loud, let all of them: Intel, AMD, IBM, SUN, Maxtor, Samsung, NEC, Hitachi, nVidia, ATI, ULi, SiS, Seagate, WD, Apple, Antec, OCZ, Kingston, Tagan, Gigabyte, Tyan, iWill, MSI etc. work on this together.