I'm not sure anyone mentioned it yet, but Defying Gravity...geez.
I would say the whole set and bridges of Starlight Express also (someone else mentioned it already) -- that set really set a high standard for me - it was the second show I saw on Broadway after A Chorus Line.
The other effect that amazed me was (well, when I saw it) Chip Zien's legs in Grand Hotel during We'll Take a Glass. I've seen the Jeter clip and my memory of Zien was about the same - wow!
Also, Jane Krakowski (enough said, but..) being lowered onto the stage in Call From the Vatican in Nine -- the stage flooding in that show was pretty cool too.
Hi, Shirley Temple Pudding.