He's complained about "MOVE FASTER POKEY" many, many times. He only ever said it once, not that you'd know, given its ubiquity (including here on TV Tropes).
Ironically, in his early romhack videos, he quotes "100 SECONDS?!" as the line everyone remembers from Kaizo; "MOVE FASTER POKEY" didn't really take off until people started doing Sparta remixes.
"Don't Eat The Mushroom" also gets this a lot. The phrase showed up in, of all places, one of the romhacks he was LPing, and his fan and fellow LPer, Chuggaaconroy, absolutely relished saying it to him when the opportunity finally arose. (Though later on, Jon managed to turn it against him).
"DEATH WATER" and "NOW I'LL SHOW YOU" are a bit more deserving of their status; even though they each appeared in just one video, Jon repeated them over and over again.
He even lampooned "DEATH WATER" himself with "CHERRY KOOL-AID".
His Super Mario TKO LP, where he encouraged his viewers to play along, record, and upload their own videos. This resulted in a surge of terrible LP videos, and was probably the key factor in the decision to Retsupurae him - note that their primary criticism is his Follow the Leader status.
He actually commented on the Retsupurae video, seeming to take it all in good taste.
So Bad It's Good: This is his opinion of Superman 64, in the sense that the game is so poorly designed and programmed that it actually becomes fun to discover different ways to break it.