Aki gets one in a dream sequence. Cid is implanting the seventh spirit into her, with Gray acting as her spiritual support. Once Aki realises this is why he's in her dream, she remarks "Gray, how sweet of you."
Sid gets a good one in as they bundle themselves into the car - about to drive through Phantom-infested Manhattan.
Sid: I gather this will be somewhat of a rough ride?
Neil: Doc, you got a talent for understatement.
After they've crashed and Ryan is wounded, Dr Sid asks him to say something to let them know he's still lucid. He replies "ouch!"
As Aki, Sid, and the Deep Eyes are imprisoned and discussing their current situation.
Grey: We need to find a way out of here.
Neil: [spouts some Technobabble about the cells being impenetrable] It's not like I can just wave a magic wand and make these bars... [the laser bars on their cells deactivate due to the city's power station having been destroyed by Phantoms that infiltrated the city]
Grey: Neil, I'm impressed.
Neil: That makes two of us.
There's something funny about Hein repeatedly barking at the computer informing him of his Explosive Overclocking, "I KNOW!!!"
Oh, by the way, Hein is voiced by James Woods, who was Hades in the Disney Hercules movie. And he's using the Zeus Cannon. Very funny in a meta sense.