Oh, hmm. I've just been playing through Infernal Machine for the first time and years, and have been pretty impressed by the sheer scale of the game, and the ingenuity of the puzzles. To pick one in particular, however...I don't know, in fact, although I'd say the whole of the Meroe level is particularly well-designed, with the light-ray puzzle at its core. That doesn't quite answer the question though.
Apart from the ToD spike room, I've also always been fond of "The Breath of God."
Come to think of it, the Max McCoy books had some great trap set pieces - the ending of Hollow Earth, with soldiers of different eras emerging from the wall and attacking was memorable, as were both the introductory segment of Secret of the Sphinx, in the tomb of Qin Shi Huang, and the same book's conclusion, beneath the sphinx with the Omega Book, was quite good.