Check the warranty.
I have a GTX 570 SC and in the case of eVGA they do cover thier cards even the OCd ones.
Its also worth checking if it will void the warranty if you OC yourself. With eVGA it does not. But again, its worth checking into. Im not sure what policies other vendors have currently.
A factory OC is good choice if you do not want to mess with/or do it your self. But as mentioned, you can also easily do it yourself.
The main difference will be the bios.
If you OC yourself, you may need to reapply the OC at boot, have a application running to apply the OC etc. becasue it may revert to default speeds.
It really depends on the card and software you choose to OC with.
With a factory OC card, the bios are different and the OC speeds are the "default" settings always. The only way to run at "reference" speed is to underclock the card intentionally.
Theres no right or wrong answer here.
If you are a die-hard OCer and want to tweak everything, a factory clocked card is really just a waste of money. As these type of users will be looking to exceed what the factory OCs offer anyway.
Otherwise they are a good option, unless you just prefer everything to run at refrence design specs. Which is fine too.
I OC myself, but seldom mess with the GPU. So I like the SuperClocked card for a slight little boost over refrence design without the need to do anything to it.
Also, the factory OC cards do offer a bit of an imporvement, but don't expect huge. Typically a couple FPS depending on the game. It isnt much.