...there's some confusion about the death of Micah, the butcher's boy. Did the Hound personally kill him? Some feel that the book is inconclusive on this point given that we know he was out with a search party but we don't see them when he returns...

Ah... Ned does see them when they return... he is in the yard when the Hound rides in, with Mycah's hewn corpse wrapped up on the back on his horse. Sandor even tells Ned how he did it -- "He ran... but not very fast." I am confused myself about how there could be confusion on this point. Yes, the Hound killed him.

others note that Arya has him in her little litany for killing Micah which suggests she knew it was him.

Arya wasn't there, but of course she knows. Presumably Ned tells her.

This one is probably trivial, but when did Benjen join the Watch? Right after the war against the Targaryens, more or less?

Pretty much, yes. Probably around about the time Ned returned from the south and Catelyn and Robb and Jon took up residence.