In Prime, I always liked the Chozo ruins. Seemed more original than just basing the area on an element (water, fire, ice). Magmoor was a little boring, and small, but cool nonetheless.
As far as the environments go, I think Tallon IV wins hands-down. When you walk through Chozo Ruins, it actually seems like you're walking through ruins of a civilization long gone. That whole game has a great setting and was immersive.
That's not to say that the games on Zebes were bad. Super Metroid had a great soundtrack that really set the mood. However, if you were going to really be walking through Brinstar, you're not going to hear the music, unless the creatures happen to naturally make sounds in MIDI that flow together in beautiful, melodic songs. If that's the case, I feel really bad for killing them.
Also, when you're walking through Zebes, could you ever imagine any kind of civilization living in those places? Those Chozo had to be crazy, placing all those spike traps and (supposed) only accessible with grapple spots. I mean, seriously. The layout and design of the Zebes games made for REALLY GOOD gameplay, but made no sense whatsoever.
I still voted for Zebes. I can't shake the nostalgia from those games.