Colbert Bump: One of the rare cases where the bumper considers this to be a bad thing, Jon expresses shame at himself for his Superman 64 let's play encouraging people to go out and buy the game.
Doing it again with Bomberman: Act Zero on his Twitch stream; whenever he does it now, there are 8-person rooms and the game reaches the top 16 viewed at the time.
Creator Backlash: ProtonJon did genuinely enjoy playing ROM hacks of Super Mario World sent in by his viewers, but he eventually got sick of them as more of the ROM hacks contained poor level designs and gimmicks. This is especially shown in Protonjon's LP of Super Mario TKO, where he expects a lot of nonsense he encountered before in other hacks and is not used to TKO having level designs that almost mirrors the quality found in official Mario games. Combined with the fact that ProtonJon wanted to LP other games, he dropped ROM hacks entirely except for one that was sent in to him by a person who wanted someone to LP it since he was dying of cancer. note Except the person was totally lying about having cancer, as ProtonJon later discovered.
Protonjon also got so angry and frustrated with people that sent him ROM hacks that abuse invisible blocks that he created an entire level made out of nothing BUT the invisible coin blocks. The level forces the player to reveal each and every hidden block to build platforms to the top, and they also have to use a springboard to reach the higher blocks. The player must then get the switch at the top and use it at the very bottom of the level to get access to the exit.
Missing Episode: His six-part LP of stage 3 from Enigmatic Mario, the second SMW romhack he did, was deleted from YouTube because they muted the audio. It can still be found there, because several people have uploaded mirror copies.
A lot of his old collaboration and challenge videos, which were never uploaded to YouTube in the first place, can be found on Google Video.
With rumours that Google Video is going to purge their archive, he finally began uploading some of these older videos, and he started off with a bang.
Old Shame: His first LP, of Kirby Super Star. He only uploaded the first part, Spring Breeze, to YouTube and refuses to upload the rest, though others have in his stead.
There's also a somewhat goofy looking photo of him when he was 18 that keeps popping up. His fans on Twitch have a tendency to refer to "18-Year-Old Jon" as though he has his own separate existence to regular Jon, much like Mario and Baby Mario.
Schedule Slip: Ever since he graduated from university in mid-2008, his updates have been erratic at best. He eventually declared the longest of these hiccups (summer 2009 to spring 2010) to be a full-fledged hiatus.
The Superman 64 LP. He is just before the halfway mark of the game as of January 2013, as stated in the Development Hell section.
He finally hit the halfway point, uploading his video of Stage 7 on January 31, 2013.
When Jon started his Yoshi's Island LP, the universe proved that it wouldn't stand for Jon posting videos regularly and frequently. Jon returned from a trip to a convention only to find that his recording and editing computer was mysteriously unable to start. Needless to say, as of the time of this writing, there hasn't been a video since.
Streisand Effect: Several games that Jon does an LP of that are bad usually has him telling people not to play said bad games because...well, they're bad and are not good or fun to play (he's playing the games to showcase just how bad they are). The most infamous example is with Superman 64 where there was a spike of people that wanted to try the game (with many actually playing it) because they wanted to experience the laughably broken game in the same way Jon did.
Throw It In: Jon's livestream of Super Mario Bros. 3 was supposed to be a typical normal run of the game. However, he accidentally kicked the game cartridge when he turned on the Retron, causing the game to be displayed with horribly glitchy graphics. Rather than fix the game, Jon decides to play the entire game in its broken state.