All the jokes are canon.Every line that is said in character and every obscure factoid that is mentioned is canon but was cut from the final movies due to issues regarding pacing, sake of drama, etc.
Malachai and Ethan Nicolle will guest riff a movie.Ethan has already done art for a Rifftrax iPad giveaway, and Axe Cop was referenced in the Clash of the Titans riff. No doubt the brothers will guest in a RiffTrax, probably one riffing a superhero movie.
The last riff on the last Twilight movie will be...... ... ... ... ... ... ..."Line?"
Reggie from the "Beginning Responsibility" short grew up and became Dan from the "Basic Job Skills: Handling Daily Problems" short.He became so ashamed of his past behavior that he changed his name, although he kept the same personality.
Disembaudio is the son of Magic Voice and CambotAfter the cast became pure energy at the end of Laserblast, Cambot and Magic Voice (finally being able to physically interact) began an affair. Magic Voice and their child stayed behind when the rest of the crew returned to the S.O.L. Not to worry, they reunited when the S.O.L. returned to Earth.
There will be a Bone-Saw joke in The Dark Knight Rises riffCome on. You'll all see it coming.
The riffers are psychic.Just look at that Hilarious in Hindsight list on the YMMV page. Unfortunately, they know from their movie expertise that revealing their abilities would have bad results, so instead they sneak small things into their riffs as hints/warnings.