In Titanic, Kevin's line of "I'm gonna sink this bitch" for Captain Théoden is taken verbatim, at the exact same scene, from way back when Mike and the bots did a short special to look over the movies that were at the Oscars that year (one of which of course was Titanic). Notable for Bill saying in an interview that for the longest time, it was one of his favorite jokes in the history of the show.
Reportedly, the chance to make this joke again is what prompted him and the team to riff on the movie at all, as they hadn't riffed on many "good" movies yet.
Star Wars Attack of the Clones has Mike saying "Into the Weenie-Mobile and off I go" as Anakin hops into a hovercar during the early assassin chase. It's a callback to the same remark in MST3K: The Movie.
Revenge of the Sith also has Mike commenting that General Grievous "needs a posture pal."
In Phantom Menace whilst continuing the Running Gag about certain aliens' notable Chinese accents one of them says (to a robot servant): 'Ahh, thank you, Number One' which is a shout out to The Navy Lark, a common phrase said by the re-occuring Chinese villain.
When Darth Vader is slaughtering the members of the Trade Federation, one of the riffers shouts "Macken!!" during a close-up of a horrified look.
Kevin:"Oh, come on, what kind of crazy director would make his movie backwards?!?!?"
A scene with Jacob in Breaking Dawn has Bill saying "Sleeping nose to anus is something I'll never get used to," then quietly whispers "wahrwilf."
In the RiffTrax Live show for Manos: The Hands of Fate, the riffing begins with Kevin saying "Wow, this really looks familiar...". He then says that it's video from his "vacation in hell".
Mike: Actually, Kevin, this looks like El Paso. Kevin: Like I said, hell.
They like to reference LOST quite a bit, particularly their disappointment with the last few seasons. A very subtle reference was made during the riff of The Dark Knight. At one point in the film, Kevin (speaking as the mayor of Gotham City) says "Get off the island, you say?" The mayor was played by Nestor Carbonell, who also played Richard Alpert on LOST.
When two characters in Attack of the Puppet People are seen watching The Amazing Colossal Man, Kevin and Bill ask Mike if it reminds him of anything. This also works as a shout out to the MST3K riff of Gamera (from the same season as The Amazing Colossal Man), where the bots asked the same thing to Joel when a rocket ship is shown taking off.