"They are a better team than they showed tonight," Knuble said. "Maybe we're not as good as we showed."
The Flyers won their third consecutive game overall after a sluggish 0-3-3 start.
"We got a great result," Knuble said. "We scored every which way. These are treats."
Antero Niittymaki stopped 24 shots in his fourth career shutout. After watching his No. 2 goaltender improve to 10-0 against the Thrashers, Philadelphia coach John Stevens believes the Flyers are beginning to match the intensity they showed last season in advancing to the Eastern Conference finals.
"We were up tempo," Stevens said. "We were a little worried because their's is a different style of play. After two emotional games against the Devils, it would've taken away from those games if we hadn't won this one."
Knuble, who made it 2-0 at 3:13 of the second period, has four goals in three games and seven points in the past five.
Philadelphia took a 3-0 lead with 14.5 seconds left in the second period on Gagne's second short-handed goal. Mike Richards set up Gagne by stepping in front of Ron Hainsey to intercept Ilya Kovalchuk's pass near the Thrashers' blue line.
Knuble's second goal of the game came on the power play and gave the Flyers a 4-0 lead 1:02 into the third. Philadelphia had an extra man because Kovalchuk was penalized for throwing his stick following his giveaway.
"We weren't ready, and from the start we didn't have the effort we wanted," Atlanta forward Colby Armstrong said. "There was a couple of good bounces for them, but at the same time the game was there for us. After they got up a few, we just kind of folded the tent."
Lupul made it 1-0 with an unassisted goal 1:20 into the game. His second goal, and fifth this season, put Philadelphia up 5-0 only 37 seconds after Knuble's third-period goal.
Kari Lehtonen's only bright moment in the Atlanta net came with 7:47 remaining when he stopped Richards' penalty shot. Hainsey gave Richards the attempt by hooking him on a breakaway.
Gagne's seventh goal this season gave the Flyers a 6-0 lead midway through the third. Glen Metropolit's first goal came on the power play with 3:40 left.
"After the success we had last season, maybe we thought it would be easy this season," Gagne said. "It's tough to get two points. Now I think we're back the way we played last season."
Gagne likes the addition of Metropolit, who signed as a free agent from Boston on July 1, to his line.
"We've got a good line here," Gagne said. "He is learning to hold the puck a little longer. I won't say we were worried about the slow start. We're back the way we played last year."
Atlanta hasn't beaten the Flyers since winning 6-5 in overtime at Philadelphia on Nov. 18, 2005.
- Thrashers rookie D Zach Bogosian, the No. 3 pick in the 2008 NHL Draft, didn't return after Philadelphia's Darroll Powe slammed him into the boards midway through the second.
- In Atlanta's end seconds later, Powe spent a few minutes on his back by the boards following a collision with Thrashers F Eric Boulton. Boulton and Philadelphia's Riley Cote were both assessed unsportsmanlike penalties at 11:55. Powe and Bogosian both skated off the ice under their own power.
- Niittymaki's previous shutout was a 1-0 victory at Florida on Dec. 30, 2007.