I think my favorite bits were:
Pretty much everything towards the end of Chamber of Secrets.
"Oh dear God I'm British! (faints)"
"Ron Weasly. Nerd, Child Murderer."
Gotta agree with the first 20 minutes of SWHS.
However my 2 favorite bits both come from Independence Day:
2: The entire first battle with the alien saucer
"Oh no you did shoot that green shit at me!" (I know that's not a riff, I just liked that line)
"The trash talking would be more effective if they hadn't just destroyed 90% of your civilization."
And culminating in:
"I hope the alien's played by Cedric the Entertainer, cause that would lead to a hilarious scene where he said 'I know you didn't dangle that parachute in my face dog."
"And then the Fresh Price of Will Smith would say "I know you don't want to be pointing a finger at me, unless you want to pull back a bloody stump."
"And then the movie could... end.", "Oh that would be great."
1: And my number one single favorite Rifftrax sequence, the entire final battle in ID4.
"Let's bronze the shoes"
"Let's polish the knob"
"Let's reinstall the OS from a slipstream disc"
"Debronze those shoes!"
"Tarnish the knob!"
"Bring the computer back to the most recent restore point prior to OS installation!"
"I takes a tough man to make a tender chicken!"'
"Take all you want, but eat all you take!
"We don't swim in your toilet, so please don't pee in our pool!"
"What did them in was their inability to come up with snappy catchphrases". "I regret some things". "See they just couldn't get the hang of it"