The Chrono series really has produced some outstanding music, and I herald Mitsuda as a musical genius because of it. I can't choose a specific favourite at all from either game... but I'll list my top-picks.
Chrono Trigger:-Singing Mountain - Reminds me of a grim determination or mourning after losing something precious
-At the Bottom of Night - Grim, sad, moving. Very fitting when played just before Lavos lands, and Ayla is offering the hand of peace and aid to Azala, who rejects, knowing that it would only prolong the Reptites' suffering.
-Determination/Chrono Trigger - In the OST I have, Determination has all the sound effects from using the Epoch to penetrate Lavos. I've listened a lot and noticed the dials and warnings become more pronounced and have more alarms going each time the view switches to the cockpit. Lots of detail! Besides, who couldn't love the defining melody that would be present in all aspects of the Chrono universe?
-Epilogue ~ To Good Friends/To Far Away Times - Together they work very well, and quite soothing!
-Corridors of Time - I absolutely
love Zeal for this song. It really gives me the impression of almost inconceivable enlightenment and wonder. Definitely among the best!
-Undersea Palace - When you hear this the first time, you're rushing to stop Zeal. It gives the distinct impression of a very advanced setting, slightly militaristic/higher class, and that time is running out before something big comes.
-World Revolution - My skin prickles when I really get into this song. It's got the perfect lead-in, as you're taking the final plunge and risking all against the one true antagonist to your quest. I sometimes wish a movie or something was made of the Inner Lavos fight -- I'd love to see it! At 01:22 as well, you get the flute instrument, symbolizing Crono and company amidst the enveloping battle against Lavos.
Chrono Cross-Time's Scar - Definitely among the top of this soundtrack. I love watching the intro over and over just for this song. I can't help but wish Mitsuda made a longer version of the latter half of the song. I'm absolutely in love with the violins in it!
-Plains of Time/Time's Grassland - Nice, Carribbean remix of the Chrono Trigger song. Soothing!
-Dreams of the Shore Near Another World/Another World - I'm a sucker for violins, what can I say? I love the chorus of this song!
-Dead Sea -
Perfect music for the region. It's enigmatic, confusing, eerie, and wonderous all at once. It really fits the setting of the Dead Sea, all the while you're gaping in wonder at just how a place like that could come to be.
-People Imprisoned by Destiny - Up there with Time's Scar. This is a very sad, unhappy theme. It gives me the distinct impression of remembrance of those lost, and the pain and suffering with it. I really wish you didn't have to defeat Miguel in Cross and leave him there to die...
-Chronopolis - Fits perfectly with the institute, with its whole eerie feeling because of the walking "ghosts." The song captures the sheer overwhelmingly techonological, yet elegance of the institution.
-Dreamwatch of Time/The Dream that Time Dreams - I agree with Zealty with this song. It really does capture the essence of the Chrono series. It's wonderous, yet gives the feeling of determination to surpass all odds and reach the final goal, and change the world for the better. I'd say that it too is with Time's Scar and People Imprisoned by Destiny in its overall prowess.