some of these may be obvious but for completeness.....
in the dead sea theres an enturane(bad spelling, the healing mechine from the future) that works just like in CT you hear the victory music, it says your HP an MP is restored, then you hear stomach grumpleing and it says your still hungery.
ozzie flea and slash are in the game as hidden bosses and you can actualy use sprig's dopplegang ability after the fight to turn into anyone of them
theres a part where you go to lucca's house.
you see a one seated verson of the epoch titled "neo-epoch"
through out the game you see ghosts of the orignal chrono trigger party (crono lucca and marle)
robo's orignal name(promethius) is used in the game for a certain thing