There IS a difference. Not as much Saigar discussion, Key shows are treated a lot better. For example, I've seen large Air threads at night be overwhelmingly positive, and the ones started during the day are flamed to oblivion. More shoujo friendly in general. In addition, night time /a/ has a lot of ronery threads, incest discussion, and loli doujin rapidsharing.
Not so much anymore, but when the show was still running, there was a certain point when there'd suddenly be a bomb of Gurren Lagann threads, and that's when you knew day had begun.