My understanding is that the major drawback with the "FakeRAID"
controllers integrated onto motherboards is that you have no method of
moving your disks from one computer to another unless you're moving to
another motherboard that has the same integrated controller. With the
Linux software RAID, you are able to move the disks to another
computer with different hardware. For some, this could be the deciding
factor between using the integrated RAID controller or Linux software
RAID.

The other drawback (again from my understanding) is that the FakeRAID
type controllers are offloading most of the RAID tasks to the system
CPU, just as software RAID would. Real RAID controllers do most of
this on the controller without going to the CPU.

I've run a handful of systems using Linux software RAID and I haven't
noticed any performance hits. On a newer system (Intel Core Duo 2
something or other...) I've also run Windows Software RAID on the same
hardware. Again I didn't notice any performance hit.

-- 
Andrew S. Zbikowski | http://andy.zibnet.us
IT Outhouse Blog Thing | http://www.itouthouse.com