Can a Mac with Thunderbolt effectively use a PCI Graphics Card using an external cage? I was wondering how good thunderbolt is for adding a beefier PCI graphics card to my MacBook Air.

If I use a PCI enclosure like this, will the card integrate with the Mac to enhance the performance of the computer or a display?
Unfortunately, there isn't currently a graphics card on the market that has a Thunderbolt-aware driver.  Without that, the solution isn't going to work.  All of the manufacturers of such enclosures have stated that there is significant demand for exactly what you're inquiring about here, and you might be best served to join some of their mailing lists to keep up with changes, i.e. cards that become compatible.  Magma for instance, has a list of "coming soon" cards on their site for their particular enclosure, but not a single graphics card.  Yet.

Don't also forget - Thunderbolt in its current state has a theoretical maximum bandwidth of 10Gbps (that's gigabits), or 1.25 gigabytes, per second and is made up of a DisplayPort signal coupled with PCIe 2.0 x4.

As you may be aware, most high end graphics cards on the market are PCI 2.0 (or even 3.0 now) and run best with an x8 slot or ideally, x16.  That kind of bandwidth — from 4GB/s on PCIe 2.0 x8 to 16GB/s on PCIe 3.0 x16 — is way over the ability of Thunderbolt.

So, even if there is eventually a card that would work, with a Thunderbolt-enabled driver that was available for your Mac - you won't likely get much more performance out of it that you couldn't get out of, say, the GeForce 650M chip in the current 15-inch Retina MacBook Pro (mid-2012).

For practicality's sake, I'd suggest thinking about how if your current laptop's graphics capabilities don't suit your needs, perhaps you might consider upgrading.  It will be likely be a long time before there's a card that will run in the configuration you are contemplating.