On a 2008 Mac Pro (a.k.a. MacPro3,1), it apparently has 2 PCIe 2.0 slots and 2 PCIe 1.1 slots. While the difference won't prevent any PCIe device from working, it does make a difference for speed.
I recently ran GPU-Z under Windows 7 and ran the load test (a '?' icon off to the right next to text about PCIe versions and number of lanes) and found that it stayed at PCIe 1.1 x16. This is with a Radeon HD 270X which is definitely PCIe 3.0 compatible, so I'm a bit surprised it didn't report 2.0!
Trying to look at Intel 5400 chipset documentation, it would seem that the chipset only supports PCIe 1.0/1.1, but all documentation on the MacPro3,1 that I've seen suggests that the first two slots support PCIe 2.0 (which I presume is direct into the CPU rather than the northbridge).
Any confirmation on the spec here? As well, why would GPU-Z only be reporting PCIe 1.1? Could it have something to do with the fact that I have a USB 3.0 card in slot 4?