There was definitely also a reference to Cloud. Two references, actually; the first one was the guy with a big sword who came by that store, and the second was "No cloud nor squall shall come between us." So, a reference to Squall as well.
I'm sure there were others, but it's been ages since I played the game. It's honestly the only of the new-school FFs that motivates me enough to replay it, but unfortunately my first disc is scratched so badly that it won't play the FMVs.