Hmm...so many to pick from...let's see....
(Not listed in any particular order of favor)
1. The Silvite colony in Skies of Arcadia when you fly up there on Fina's ship. It was a very Zeal-esque place, except, well...near completely deserted, I believe. It was magical to fly up past the skies and the stars to appear on this strange piece of incomprehensible technology, and hearing what the elders had to say...it was amazing.
2. Mars Lightouse in Golden Sun The lost Age. It really gave you a sense of desperation to climb, as if it was not lit, Prox would have been sucked off the edge of the world, and would continue to do so until the entire surface was gone. Plus, I found the snow whirling everytime you went to the outside to be a nice touch as well.
3. 1000 A.D., overworld. With my favorite Chrono Trigger piece (Memories of Green) playing, I really felt a sens of freedom and mysticality just exploring the 1000 A.D. overworld (especially in that desert-region...with no scenery to break the clouds, you feel like you can fly.)
4. The Dead Sea - all. After playing through mostly boring bits of tying up loose ends, you're treated to one of the most impressive places of the game, and one of them that convinces me that when people say Chrono Cross has no connections to Chrono Trigger has not fully played the game. Seeing a future that was erased from time..that YOU erased playing Chrono Trigger brought a feeling of awe. Walking on massive waves frozen in time as the futuristic world suffers the wrath of Lavos (one of the best moments = the room with the Lithosphere report of Lavos. You can see the waves in mid rush of the room, which really nails the point of the apocalypse home.) Other touches such as the room with the train and the boarding pass to Arris Dome add to it, as it connects to Chrono Trigger in ways that most of the rest of the game fails to. The enertron as well was fun with the classic "But you're still hungry" line after it. And the Leene's bell scene with Miguel and the ghosts/dream projections...that, to me, was the most emotional event in the game. Hearing the sad music play while you fight a battle that nobody wants to fight but is bound by fate, onlooked by the childlike ghosts that mimed the heroes of Chrono Trigger, spawning many debates over their fates after Chrono Trigger. To put it simply, this place was brilliant.
