In my desktop, they face out, but with the GPU right on top of them, I have to make sure the SATA cables don't hit the fans. Because the clearances are fairly tight, I usually have to pull the GPU if I'm going to do anything drastic with my drive cables... it's just easier that way.
In my game rig, they face sideways (towards the front) and while that keeps the cables away from the GPU fan, I can't get my finger in behind the GPU to release the SATA catch... and have to pull the GPU.
I do prefer the aesthetics and cable management of the side-facing ports, however, I just wish they could line them singly along the mobo edge (although I understand why they can't.)