Can I use two GPUs With a Mac Pro 3,1?

Don't buy a 2008 and definitely don't buy older than that.

Get a 2009 Mac Pro 4,1 or later, for better processors, faster busses, faster PCIe slots, and better memory.

The silver tower mac Pro has 75W available from each slot, and two 75W 6-pin aux connectors total.

Many gamers are buying PCs that are way cheaper than the server-class Mac Pro silver tower with error-correcting memory.

Two GPUs on a Mac do NOT cross-connect with crossfire, even if the physical connection is present. It is simply not supported by Mac OS X. Unless your software does it manually (unlikely) the benefits of a second GPU for gaming will be small.

A Mac makes a poor gaming machine compared to custom PCs. 😟

As Grant says OS X does not support AMD's Crossfire system for linking two video cards, nor does it support Nvidia's SLI equivalent. Your best option to get the best video performance is to get one top end video card. This would be currently either an Nvidia GTX-980 or GTX-980Ti, or an AMD R9 290x. According to this and others http://forums.macrumors.com/threads/anyone-try-a-r9-390x-yet.1916259/ the R9 390x is not supported properly by Mac drivers.

Some people do use a very basic video card to provide Mac boot screen capabilities e.g. the GT-120 and a second much better card (like above) for performance.

The classic Mac Pro can provide 75W from the PCI slot plus 75W from each of the two 6-pin PCI cables making a total of 225W available to a single video card. Some video cards need more than this and would have problems. In which case fitting a second power supply externally or internally in the optical bay is the only solution.

The GT-120 video card needs no additional power cables so could be used even with a second video card that uses both 6-pin cables.