Actually happened to me a few weeks ago, all 4 of my PS3 controllers stopped recognizing my machine. 2 DS3's and 2 Original PS3 controllers. Another PS3 owner was having the same exact problem (oddly enough at the exact same time I was), and this was how I fixed it.

"I've no idea how this happened, but I fixed it by simply turning my PS3 off, and then back on. Plug your controller into the PS3 and then hit the PS button, the controller should assign itself a slot, and once unplugged should remain keyed to the PS3. I was watching a movie when this all happened, so I've absolutely no clue how it could've occurred. But, that fixed it.

Very strange indeed, hope that helps though."  - Pulled from my response on the PS Forums

I had the same issue with two of ps3 controller, it will eventually just stop working. I had to replace both my original ps3 controllers with the latest ones.

I even pulled both of them to bits and tried swapping the batteries from one the the other but was to no avail.

Not sure that's accurate, the two DS2's I have that originally came with my Fat 60g, have been running since launch, and I've only had the one hiccup, which was fixed by turning the PS3 off connecting the controllers and turning it back on.