Currently it is server/workstation boards that are running 3.3V slots.
This is kind of foggy in my mind, but if I remember correctly, PCI 2.1 is 5V only, 2.2 will support both 3.3V and legacy 5V PCI products as well, but PCI 2.3 (maybe??) and onwards will only run at 3.3V.
All of the current Dual Athlon boards have 64bit/66MHz busses on them, and will run cards at 3.3V. The 32bit slots on these boards are still 5V only though.
Ian