I've heard about the C63 (and M156 engine in general) headbolt issues although I'm not too sure on how widespread or how severe the problem is. I believe forums and the Internet in general tend blow any such issues way out of proportion and make it out to be far more widespread than they truly are.
I remember reading about rod bearing failure issues with the S65 motor a long time ago and although people made it out to be a huge issue that was rumoured to affect all S65 engines at the time, it appears that many M3's have racked up plenty of km's since then and it didn't turn out to be a widespread issue with the S65 engine
A quick search regarding the rod bearing issues can reveals this thread which provides for a decent read.
I'd personally swing for the C63 for a daily driver myself as I spend a whole heap of time in stop start traffic and love the torque of the M156's but in saying that, I've spent quite a bit of time driving a friend's 6MT E92 M3 and it is an unbelievably good car too! The character and experience of an M car is totally different to a BMW series car
The best advice I could give is to drive both cars and think about how you intend to use them and go from there. Good luck with your search