Obviously if a bolt has stretched or is corroded, bent, or visually damaged, by all means throw it away. If you are not sure, you can measure the hardness, check its structure and grade (destructive tests, in general) and chemistry to see where you are. And as far as fatigue one must know if the stress on it is in the fatigue range, and so is temperature, that has to be high enough to affect the metal. All of these tests make sense in a lab, but practically it's much cheaper and easier to use new fasteners, so I don't have a problem with that.
I look at it this way, there are certain fasteners in an engine that, if they fail, the cost to repair far outweighs the cost to initially replace. Rod and main bolts come to mind. Head bolts don't quite fall into that category for me but the thought of hanging over a fender wrasslin' a head off because the headgasket failed due to a soft headbolt puts those into the replace category for me.
The rest, not so much.
