Rainbow Caverns, and the Mine Train in general, was what sold me on Disneyland as a kid. I even tried to recreate a miniature version of the colored water in my backyard with my own blacklight. It only lasted one night and was just a couple of pools of color that I manually poured into, but it made me appreciate how complicated of a job it was to build that. They had six separate plumbing systems, one for each color. There were some parts where the train passed over the colored water, and there were separate channels of color, maybe 4 or 5 inches wide, running along side of each other. They passed right under the track. One blue, the next one orange, the next one green, etc. All glowing brightly and pretty opaque, not watery, they must have dumped tons of the color agent into the water.
I still have never seen anything like it since then. The scene in the first lift of Big Thunder does not remind me of it, nor does the Calico Mine Train at Knotts. The Rainbow Caverns was entirely dark and illuminated only by blacklight, there were no colored lights. I remember it was pretty loud with all the splashing sound made by the various fountains and waterfalls. Above all that you could hear the music. It was also cool, with fans blowing cool air around. The first 30 seconds of your trip through it there was nothing, it was totally dark to give your eyes time to adjust after the bright sunlight of the living desert. Then the pools and fountains and rivers started to appear. Since it was so dark you could not see the ceiling or any of the texture of the walls. The stalactites you see in the video were just silhouettes. The video above used a light attached to the camera to make it brighter for the film to record it, but it was really dark and the only thing you could see was the colored fluorescent water and whatever it could illuminate with its feeble light.
There were a couple of signs, also fluorescent and lit only by black light, one saying "Witch's Cauldron" which scared us, but fortunately the witch always had the day off and was never seen. The very last thing before you left the caverns was a set of 6 waterfalls side by side, one of each color, and that was Rainbow Falls. Then you left the caverns and you were back out in the little town of Rainbow Ridge (the buildings are still there now behind Big Thunder).
From 1959 to 1963, there was a Mineral Hall to the right of the the Mine Train loading area, and you could go in there and buy rock samples and see examples of the fluorescent minerals under black light. You could even buy black lights. The employees who worked in that section wore black so they wouldn't be too bright under the black lights. The building is still there now, but I think it is just used for storage or something and only an upper window is etched with the name "Mineral Hall" as a tribute.
This page has some more pictures of Rainbow Caverns, some of them are pretty fuzzy but if you look over them you can get a general idea:
Index of /MineTrain/RainbowCaverns
The music played in the Rainbow Caverns is available on the "Musical History of Disneyland" CD set that you can buy but it's something like $70 new. You can also listen to it here, the music in this clip is the exact music that played continuously in the Rainbow Caverns:
[ame="http://www.youtube.com/watch?v=qr0jk48veZk"]YouTube - 1960z Disneyland 8mm family footage with Rainbow Caverns song[/ame]