Here's my
on the subject...
Fakeraid (mobo's so-called raid controllers as well as 99% of those cheap raid add-on cards) are not so reliable, I had 3 bad experiences in the last 10 years with these, with fried controllers and one of them that became nuts and corrupted the whole array... I will never buy again one of these add-on cards (either PCI or PCI-e) for their RAID capabilities. A real RAID (hardware) controller costs lots of $ but is more reliable. There is a reason why some goes for $39 while others go for $799...
Like I just said, if you want hardware controlled RAID, I would uggest going with real controllers, but be ready to spend lots of money. I really don't think for home usage it is worth it.
The problem with hardware (either fakeraid or real raid) is that you add hardware components to the whole system... By adding such extra hardware layer, you increase the probability of failure and decrease the reliability of the system. That's why I said for hardware controlled RAID, I would go with commercial class because these components have a better documented reliability and apparently their quality control (I did not confirm this) is supposed to be better.
I personally use software RAID (using mdadm). I recently lost a almost brand new WD caviar green and most of the data that was on it. My mobo has a fakeraid controller, but like I always do, I enter the bios and setup the controller as standard SATA controller or depending on your BIOS, deactivate it. Then I setup a software raid 1 array with 2 hard drives. My whole system runs on RAID1 while other partitions are only backed up using rsnapshot.
As far as I know, the main differences are speed, performance and reliability. Hardware raid (real one) might be better in the two first, but I believe software RAID is more reliable. Again I should mention instantaneous reliability VS long term reliability...
With fakeraid, I believe you dont have the performance of real raid while you have lower reliability. You get the worst of both worlds.
I might be wrong but this is my experience... I hope it helped.