What causes black spots on silver? I've seen some really nice early silver coinage, but a couple small black spots take away from the quality,
It's pretty simple, when silver tones it eventually turns black. That is the nature of silver. As for there being black spots instead of the entire coin being black, rather obviously at some point something got on the coin that caused those tiny areas to tone faster than the rest of the coin. That's the most common reason for spots.
If you are referring to the dimes in this thread - http://www.cointalk.com/t218720-2/ - those are not what I would call "spots". But yes, that is black toning on 2 of those dimes.
Black spots on silver are generally caused by the silver reacting with sulfur. Silver Sulfide is black as are many of the other sulfides.