Despite the frequent Schedule Slip and relative infancy of his Superman 64 LP it counts as one solely for the reason that as of yet no complete playthrough of this game exists on the Internet (in fact, it's next to impossible to find ANY footage of the game past the infamous rings). This effort was enough to make the LP noticed by Kotaku.
In episode 5 of Superman 64, he demonstrates the option to reduce screen size to 20% of normal - and despite having only a 15" monitor which is already distorted by his video capture technology, proceeds to fly through the entire first section of rings without losing a single life.
And beating Game BoySuperman, in its entirety, faster than just one level of Superman 64.
This is less a testament to Jon's awesomeness than it is to Superman 64's awfulness.
Uploading before Chuggaaconroy counts as one. Even Chugga noted this in his Facebook post.
Chugga: Jon uploaded before me? IT REALLY IS THE END OF THE WORLD!
When he fights the Ark Reactor with Jirard (after first being demolished by Hammer Force and continuing), the duo get to Runner Force and then Jirard gets cornered and finished off. ProtonJon, being stuck with flare (Fire and Force), has trouble dealing damage to him. Runner Force hits him while he's at 8 Vitality... bringing Jon down to exactly 1 hit point. He immediately finishes off Runner Force.
This gets turned around at the final boss, Golden Silver, where Jon is the one that dies and Jirard's the one that kills the boss.
The Notte Luminosa finale. By this point, it's revealed that the Romhack creator who wanted someone to LP his game as a dying wish was actually not dying at all, and was lying. The way Jon handled the situation was very adult and tactful, and it would be tempting to just unload on the guy, but Jon didn't.
Jon and Jake play Resident Evil 5. In part 4, they're trying to shoot the driver of a truck about to run them over; twice, Jake gets killed. On the third attempt, he shoots the driver, gets run over by the truck...and comes out the other side without losing much health.
Jon: MOVE BACK YOU IDIOT!
Jake: (shoots the driver) Nope, cause I killed him. (gets run over by the truck and stands up) Problem? (starts shooting enemies casually)
Jon: (after a Stunned Silence) Are-wh-are you...okay, I guess you're okay, that's good. (Jake starts cracking up) I saw you get run over by a vehicle, and then come out the other side, so I was a little concerned!
Jon sniping an emblem from the other side of the map in part 14. On his first attempt.
In part 22, after using up all his rifle bullets shooting an emblem, Jon only has his handgun left to try and shoot at a distant enemy they need to take out for the plot to progress. He does it on his first shot.
Managing to defeat, rather than stall out Wesker and Jill also counts.
In the finale, Jon and Jake run out of ammo while fighting the Final Boss and so attempt to take him on with just a knife and a stun baton...and it actually works for a while until they get killed by one of his tornado attacks.
Jake stabbing the emblem across a pit in the DLC, after being sure that he couldn't reach. The ensuing cry was worthy of the Game Grumps, so much so that Jon obviously had to tone it down in editing.
In episode 33, after having a lot of trouble with being sniped at by a turret, Jake asks Jon to try and take it out with his rifle, and shows Jon where it is by spraying his machine gun vaguely in the direction. Jon sights in on it...only to find that Jake somehow managed to kill the turret guy with his machine gun spray from a distance.
Part 2 of Desperate Escape has Jon tackling a majini through a shack, shattering it on contact as said majini gets thrown off a cliff, complete with a football horn sound and the word "SACKED!!!"
Jon: THROUGH THE BUILDING!
Jake: I am slightly becoming more attracted to you.
The entire part 2 of Desperate Escape consists of Jon and Jake performing tons of physical moves on the enemies like iron tackles, suplexes, hammerblows, etc. Some of the moves also resulted in Your Head Asplode.
In the Collab "A Tale of Four Idiots" Castle Crushers series, one of the other players teases Jon about having flashbacks to Battletoads. Jon replies by nonchalantly saying: "Ah, whatever, I got over my Battletoads flashbacks. I'm one with the Toad now."
Jon ends up playing a nightmarishly glitched version of Super Mario 3 on a Retron and decides to continue out of curiosity. As several commenters point out, he manages to play Mario 3 better when he can't see anything than many people can the normal game!