I actually just did this test about 3 months ago. And although the test was flawed (which I will explain) my general consensus is that at this point in time FW800 is still very much valid. I do pro audio stuff and it makes sense not only as a computer interface for a Mac but also as a market thing because there are still new interfaces being made with FW800. Thunderbolt exists, I think there may be 2 interfaces setup to use it, only one of which is actually native TB. I seem to remember one TB device that actually uses a USB of FW controller to adapt it.
I bought a CalDigit USB 3.0 Express34 card for a 2006 MBP 2.16 ghz 17 inch. It's purpose was to run a USB 3.0 drive as an audio drive for Pro Tools. The result was that I got a ton of DAE 35 error messages because Pro Tools wasn't being allowed to access the drive like it wanted to for some reason, most like because of a poorly designed driver. I have switched to an OWC flush mounted eSata card and have yet to have a single issue. It's been about 3 months now.
I have an Avastor drive with USB 3.0 (and 2.0), eSata, FW400 and FW800. I did a transfer test of a big chunk of data (maybe 9 gigs - I don't remember), onto and off-of the Avastor drive - off-of/onto the internal MBP drive, respectively. All transfers occured between those two drives. I did six individual transfers using native FW800, eSata with the OWC card, and the final time through USB 3.0 using the Caldigit card. It should be noted that the Caldigit USB 3.0 card uses drivers, whereas the OWC eSata does not.
OSX estimated the transfer time for USB 3.0 and FW800 to be the same at about 12 minutes. The eSata card cCame in at 9 minutes. I did a stopwatch time on my phone and those numbers seemed pretty darn accurate.
Here's the first catch - obviously the USB 3.0 card is NOT native and uses a driver, the eSata is a pnp, driverless adapter. FW800 is native all the way. I think that Apple will adapt USB 3.0 at some point, and I think somepoint soon. PCs are already shipping with TB. Judging by the FW800 performance and the theoretical bandwidth of all three protocols - native USB 3.0 on a Mac would be very fast indeed.
Here's the other catch - I had so many **** issues with the USB 3.0 card. I have no issues with FW or eSata. Apple will intentionally skirt the protocol for market reasons, even though it might be the most kick *** storage alternative to both. As they can obviously integrate protocols well into OSX and the hardware. It shoul dalso be noted that some USB 2.0 interfaces in the audio world FAR outperform some FW400 devices. There are some stupidly low latencies in some USB 2.0 controllers.
All I want is a TB interface and 3 native USB 3.0 ports for an Audio drive, Backup drive, and iLok. And keep the Express34 card slot Apple that thing has saved my ***!
Hope this helped.