Director Steven Spielberg asked, "What if they (the aliens) go the other way: they come under ground instead of outer space?" Usually, going the opposite direction of what has been done in the past proves to be successful, it was stated.
The key to those big, scary tripods was the three legs," according to Doug Chiang of the art department. He was the main speaker in this bonus feature. "The three legs symbolized how much different these beings were culturally from life on our planet, where everyone or everything is on two or four legs," he explained.
Spielberg also wanted them scary, not just some big machines. The aliens he wanted "creepy," and to movie in a smooth, yet odd, way. All of that, he got, as those who saw this movie knows.
The special-effects, in my opinion, are the draw to the film and the only reason I've seen the movie a couple of times. Chiang and his crew did an awesome job creating them.