By imbedded RAID controllers you mean on the motherboard right?
Well, I have an imbedded Fastrack100 on my Asus A7V133. It is by most purposes the same exact thing that Promise sells on its separate RAID card. The only difference between the two is the BIOS. However, you can easily use the full Promise Fastrack100 BIOS on the A7V133 (just need to tweak it a bit). Also, the full Promise drivers will work fine on the imbedded chip.
So, though I have not directly compared the performance of each, it is safe to say that imbedded vs. add-on RAID really has no performance differences.