The only difference I've noticed is that the boot up from a "cold start" seems to take longer than with my 4S but it's slower than the new phone anyway.
I have 2 iPhone 3GS, both are on 6.0.1 & working decently. Battery life is ok & it's not that slow.
About upgrading to 6.0.1, it depends. Are you currently on 5.1.1? If so, do NOT upgrade. I kinda regret upgrading, because iOS 6 does not bring much useful features to the 3GS. If you are on 5.1.1, it's better to stay there.