ATI Linux driver support has improved dramatically from several years ago. I have a number of machines with ATI cards (3870, 24-something, a 690 based uATX board with integrated graphics and a Dell with embedded ATI graphics). The ATI installer is pretty bulletproof and the performance is good. Not at all like back in the days of the 9700. I used to worry about using ATI with Linux: I do not anymore.
I have read that neither ATI nor Nvidia supports CF/SLI under Linux. I don't know if it is true. Can anyone confirm or refute?
The driver is built around a kernel module and if the kernel is updated then the graphics driver must be reinstalled, which is a pain. But Nvidia is the same in this regard.
FWIW, ATI's CAL or Stream Computing SDK also runs on Linux now. As much as I have played with it, it seems to work well (I have not had as much experience with CAL as with CUDA though.)
AFAIK - as of about 8 months ago - neither CAL nor CUDA will use both GPUs if the GPUs are in Crossfire/SLI mode. This would be a problem with ATI or Nvidia. If the cards are not paired up then both are available - I've verified this with an Nvidia 8600 and 8800 in the same box, and it is what ATI says in it's docs.