Daniel,
Assuming no damaged threads, shanks or heads, the physical part goes like this.
If the application was subject to high cyclical loading, and bolt was not preloaded to a stress higher than the cyclical load, the bolt has accumlated stress cycles and should be replaced just to be prudent. Actually a lot of general prudence is in order, because the above would be the result of poor design, poor installation, or outright overstress.
If the application was subject to high cyclical loading, but the bolt was preloaded to a stress higher than the expected cyclical load, the bolt can be re-used....but nobody does. Connecting rod bolts are a good example.
If the application pretty much applied a steady stress to the bolt, and that stress did not exceed its yield strength (check the root thread for stretch), it can be re-used. Most of the screws and bolts we use are in this group.