From "The Equation": Peter threatens a man who wants to recommit Walter to the mental facility. "You may think you know what he's capable of, but you have no idea what I'm capable of."
From "The No-Brainer": Broyles giving Sanford Harris the verbal beatdown the man deserved. After two episodes of harris abusing his new position to get revenge on Olivia, Broyles not only commends her for completing a case with Harris breathing down her neck, but then blasts Harris for trying to take down Olivia for transparently petty reasons. He then follows it up by out and out telling harris that if he keeps harrasing Olivia, he will have to deal with broyles and that "All the red tape in the world won't stop me".
Mister David RobertJones gets one for breaking out of a high-security German penitentiary using a teleporter assembled from parts stolen by having his goons walk through the walls of the safes and banks that stored them. Oh, and did we mention that the wall-passing machine used an equation solved by a hypnotized child savant?
And another is season 4, when he escaped a joint Fringe tracking team that had locators in his bloodstream:
David Robert Jones: Hello! Would you like some money?
From "Over There, Part 2": In all honesty, Bellydid try to tell the Alternate Fringe division agents about the new features of the Model 77.
Olivia breaking out in "Bound". Making it finally clear that this introverted and low-key woman is in fact a Bad Ass after all.
Fauxlivia also rescues herself in "Bloodline."
Walter threatening Olivia's abusive stepfather ishe COOLEST thing he's ever done and it shows that he really did have a heart for the kids that were left in his care.
On a meta level, the kids playing Olivia and Peter. Someone paid attention to all of the grown-up versions little mannerisms, and you can see some of them in the kids too.
Anna Torv's scary good impression of Leonard Nimoy.
And one for Belivia himself... for pulling a stunt like that off.
Animated Peter beating up a dozen lab coated zombies on top of Bell's WTC office and then escaping on a zeppelin It's that kind of episode.
From "The Day We Died": Future Olivia, now in control of her abilities, casually preventing a box from smashing into the floor by making it float in the air and slowly decend using her mind.
In "Novation" Peter rewires the speaker in his cell so he can eavesdrop on the Fringe division then uses his knowledge of the shapeshifters to more or less blackmailing them into bringing Walter back. He might been locked in a cell and a stranger to his friends now, but he is not useless.
Olivia "turns on the lights" in The End of All Things just like David Robert Jones wanted. She doesn't just turn on the little lightbox contraption. She turns on the other lights in the prison as well. And fries a mook like crispy bacon while she's at.
This one plus the scene in Enemy of My Enemy wherein Peter reveals to David Robert Jones how much he knows about him, and that he remembers killing him. It is just all too satisfying to see how the face of the The Chessmaster and Smug Snake Jones seems to say "WTF??" for once, if only for a split second!
Fauxlivia shows off her Olympic level marksmanship by counter-sniping a Shapeshifter. Who was on top of a building. Through a hole about a foot and a half in diameter. While he was running.
From the Comic-Con season 5 trailer. Which promises science based badassery from the Bishop family.
Peter: We need to keep those bald headed bastards occupied.
Olivia: What do you have in mind?
Peter: I think it's time we caused a few Fringe Events of our own.
Nina and Walter outplaying William Bell in the season 4 final. Nina uses her hinted at but previously unseen knowledge of mad science, that reassuring voice of hers and her resources at Massive Dynamic to track him down. Walter finds the loophole in the diabolical plan and ends up saving not only the two universes but Olivia as well.
Observer: I think of you as I would an ant colony as I pass by it. I don't care about the workings of the colony, why one ant is mad at or another or why one ant would kill another or not. To me, it is insignificant. And like an ant colony, you are oblivious to your limitations. You think the black over your head is dark skies... when it is really our shoe.
The trend continues onto the next episode with some pretty awesome and goddamn horrifyingPeter moments where he coldly tracks down each and every single one of Windmark's top lieutenants and murders them all by using probabilities and some gambits that would make Xanatos proud. And now he's going for Windmark himself.
If you look closely at the trailer for "The Human Kind", you can see that he's predicted Windmark finding the timelines in Etta's house and wrote "YOU ARE HERE 5:42" on the board, just to mess with him. It's good to know that he's retained the ability to Troll.
Peter versus Windmark. They proceed to beat the crap out of each other with moves right out of the Matrix. Peter only retreats when another Observer injures him.
Nina: Do you know why you tilt your head in that way? It's an involuntary reflex in your physiology. It changes the angle at which sound waves hit the eardrum, allowing in more stimuli. Like a lizard. I've studied them, too. Intriguing character. Their brains have evolved over 320 million years yet for all their evolution, they form no bonds. Love does not exist for them. They are incapable of dreaming, of contemplating beauty, of knowing something greater than themselves, not unlike your kind. The experiments we conducted right here in this lab yielded a surprising result, because for all your years of evolution, you inadvertently developed and honed primitive instincts that we moved beyond long ago. So in reality, you're the animal.
Her final words have a pretty awesome double meaning to it. "I know." She knows the plan now. She knows that she won't live to betray Olivia and the Fringe Team. She knows that Windmark is totally screwed.