Hansen, 22, split 27.93 seconds at the 50-metre turn before powering home in 59.30 seconds, almost half a second faster than the former world record of 59.78 set last year by Japan's Kosuke Kitajima at the World Championships in Barcelona.
Four years ago at the trials, Hansen finished third in the 100 and 200 metres breaststroke, missing a Sydney Olympic berth each time by hundredths of a second.
"After 2000, I was a man on a mission," Hansen said. "The emotions from that meet have been with me every day of the last four years."
Phelps, who set a world record in the 400 metres individual medley on Wednesday, swam the fastest time in the 200 metres freestyle semi-finals on Thursday, clocking 1:47.42.
Klete Keller, who broke Phelps's American record in the 400 metres freestyle yesterday, was close behind on 1:47.65.
Coughlin posted the fastest semi-final time in the women's 100 metres backstroke with 1:00.91. She holds the world record at 59.58
Unheralded Rachel Komisarz, 27, came from behind to nip Jenny Thompson in the women's 100 metres butterfly, touching in 58.77 seconds to Thompson's 58.98.
Kaitlin Sandeno (4:08.07) and Kalyn Keller (4:09.78), Klete Keller's younger sister, took the two Olympic berths in the 400 metres freestyle. Defending Olympic champion Brooke Bennett finished seventh.
The trials run until July 14.