It looked like a real punch to me. Like harlemhustla, I've also seen the punch from different angles, and it definitely looks like a legit KO punch. Liston never saw it coming, and the fact that he was coming inside on Ali and got countered makes the punch have even more effect. Ali's handspeed was godly, it doesn't surprise me at all that a lot people didn't see the punch, especially from the angle it's usually shown from.
But hey, you wanna talk about a real phantom punch:
http://www.youtube.com/watch?v=0zsLXOc65dw
Courtesy of one Luisito Espinosa, former bantamweight and featherweight champion, who is now reportedly working at a Costco in San Francisco.