I'm not making light of the situation if there is something wrong with your pup, but it reminds me of the "Everybody Loves Raymond" episode when Ray gives Deborah some "alone" time, spies on her and finds her crying. When he asks her why she says sometimes it feels good to have a good cry...it was a funny episode. Maybe your little guy was just getting in touch with his emotions
If nothing else seems to be bothering him, he might just be a little lonely. Some dogs take a little longer than usual to get over being crated or "put away" ...and some never really do get over it. Hope someone can help you out!