What was your favorite part? I assume you're talking about Chrono Trigger?
I have a lot of fond (childhood) memories with this game, but I think arriving in 2300ad that first time, fighting the Guardian, and retrieving the seeds was the first part of the game where I really felt something was special.
Also -- beating Magus and thinking I was at the end of the game, only to discover that I was nowhere near the end... that was awesome.