I read this really great Fan Fic once that was really long but really tied in Chrono Trigger really well to Chrono Cross. I thought it was rather neat so I saved the link. Here it is.

http://www.fanfiction.net/s/620490/4/

I know it doesn't say all the references between the games, but it's a really good fanfic that connects the two stories by filling in the time between the games.

Danny