Scully dominated the 40km points race to take gold with fellow Kiwi Aaron Gate claiming bronze, while in the 1000m time trial Simon van Velthooven won silver and Matt Archibald bronze.
Scully won six of the 16 sprints to finish comfortably ahead on 98 points in his race, 14 clear of silver medal winner Peter Kennaugh, of the Isle of Man and Gate (82pts).
Velthooven and Archibald both broke the old Commonwealth Games record in the kilo time trial but had to settle for the minor medals behind defending champion Scott Sunderland of Australia.
Archibald, riding in the sixth heat, initially held the Games record with his one minute 1.162 seconds – which eclipsed his previous personal best time by six seconds.
But in the thrilling finale between Sunderland and van Velthooven, the Australian flew home to take gold in 1min 0.675s with van Velthooven finishing in a time of 1min 1.060s.
It brought the cyclists medal haul to nine overall so far.
The judo team has also been one of the success stories of the Games and they added another two medals on day three to lift their overall tally to five, which equals their best-ever haul in Auckland in 1990.
Tim Slyfield and Jason Koster each won bronze in the under-100kg division.
Slyfield beat India's Sahil Pathanian while Koster defeated long-time rival, Australian Duke Didier.
Earlier in the Games, Darcina Manuel won a bronze while Moira de Villiers and Adrian Leat won silvers.
But it was another disappointing day for the New Zealand triathletes as Ryan Sissons, Tony Dodds, Nicky Samuels and Andrea Hewitt again failed to get a medal after finishing fifth in the team event.
In the pool, the medal drought continued with Glenn Snyders finishing fifth in the 100m breaststroke, which was won by England's Adam Peaty, and the women's 4x200m freestyle relay team coming home fourth as Australia took gold.
Elsewhere, the New Zealand sevens team booked a quarterfinal showdown with Kenya after coming through the pool stages unbeaten. They easily accounted for Canada (39-0) and Barbados (59-0) but were given a scare by Scotland before hanging on for a 17-14 win.