there are three way of doing raid... pure software, pure hardware, and hybrid.
Pure software aka OS,level raid (ex: ZFS on osol, windows based raid, linux based): slow (comparatively), reliable, free, no single point of failure, easily migrateable, etc
I use pure software raid.
Pure hardware (ex: 300+$ controllers): blazing fast, single point of failure (can be repaired by exact replacement of potentially hard to find hardware in the future), proprietary, non migrateable, etc
Hybrid (motherboards) - all the disadvantages of pure software, all the disadvantages of pure hardware, none of the benefits of either, and a many new disadvantages unique to hybrid (such as array loss on cmos clear) and it being even slower than the pure software implementation.
Hybrid (mobo raid) has one and only one unique advantage... Windows cannot be booted off of a RAID software array (some other oses can!), only a pure hardware or hybrid raid can be used as a windows boot drive. And the pure hardware is expensive while the hybrid is usually "free" (included in mobo price and has a ton of disadvantages and risks)
Anyone that knows anything would tell you to never, ever, ever! use mobo based raid. Actually I went against such advice from several professionals (what with me being a professional myself, and mostly thinking "it can't be THAT bad")... well i was wrong, it was worse than I ever imagined, i didn't give up easily either... i tried various configurations such as raid5 and raid1 on a variety of mobos over of the years, nforce 2, 4, 5, and intel chips (ICH#R)... all were bitter disappointments despite having been given plenty of time