This is one of the cases that's always fascinated me, due to how many people were witnesses to the event. I think we're beyond the point of asking whether it was something real or not, and more towards what the hell it was. Although there seems to be some confusion still regarding what was seen. From Wikipedia:
There were allegedly two distinct events involved in the incident: a triangular formation of lights seen to pass over the state, and a series of stationary lights seen in the Phoenix area. The U.S. Air Force later identified the second group of lights as flares dropped by A-10 Warthog aircraft that were on training exercises at the Barry Goldwater Range in southwest Arizona.
The description of the huge triangular craft reminds me of the black triangle UFOs people see all over the place, what with the shape and the lights. Begs the question if it's based on the same type of technology. Although the Phoenix craft was just kind of like more gliding across the sky, rather than the triangles which as far as I know just zip across the sky at breakneck speed. Size limitation perhaps. Also, neither types of craft make any sound apparently.
So if this was some super secret military aircraft why would they deliberately fly it across an entire city at a relatievely low altitude where it could be seen by tens of thousands of people? Did they just need to get it from point A to point B and assume nobody would see it?
Even if, for the sake of argument, it was some kind of different higher intelligence it'd be a bit strange to fly across an indigenous population center and just be like "Hey, what's up? See ya later!". But what do we know?
(As a sidenote, I seem to remember hearing some folks saying they got a strange sort of ulterior sensation to go outside and look at the sky as it passed over, but might just be people wanting to put some extra flair to their story)