Chrono Trigger is my favorite soundtrack of all time. It beats Radical Dreamers and Chrono Cross.
I think it's the most memorable, and I may be a bit biased, as Chrono Trigger holds a special place in my heart (as the first true RPG I ever played, plus I was a young child when I played it). There are some really stand out tracks that are just completely epic for various reasons... Silent Light is so dark and mysterious, Chrono Trigger (theme song) is so epic and fist pumpin' radical, Memories of Green is haunting and serene, Wind Scene has a darkness and curiosity that screams "things aren't right", Brink of Time is majestic and yet foreboding, Sealed Door is so bittersweet, etc... I think each of these themes is a truly standout example of emotion in the video game art form. These are just a few themes off the top of my head and there are just so many great, memorable songs in Chrono Trigger.
I think overall there are more memorable themes in Chrono Trigger than the other two. And the thing is, I don't think many of the Chrono Trigger themes translate well to orchestration. This is where the Chrono Cross soundtrack really shines. Chrono Trigger, because it's in mini-form, is simply able to do more than the Chrono Cross soundtrack.
I haven't given the Radical Dreamers soundtrack enough time to really consider it, though...