A pre-powers Peter standing up to a bullying Flash, even though he knows it means getting his ass kicked. Gwen gets one too by getting him to stop with little more than a disapproving word and a look. "I'm still not taking the picture."
The NYPD SWAT opening fire on the Lizard in a coordinated mass effort rarely seen in such films. It didn't take, but still...
Uncle Ben staring down the robber before going for his gun.
After spending most of his hero career basically chasing down anyone who looks like Uncle Ben's killer and just beating the crap out of them, he finally does something that's for the sake of someone else when he saves a bunch of cars from flying over the edge of a bridge. After saving a child and seeing the kid's father holding him, it's like Uncle Ben's words about responsibility click. And to cement the awesome, when asked who he is, he says (for the first time anyone says it in the film) "Spider-Man."
While looking for the Lizard in the sewers, Peter shoots his webs in several directions and ties them together so that he'll be notified when something touches the strings. In other words, he's making a spiderweb.
Spidey vs the Lizard. Doesn't matter which fight. Every time they fight, Spidey fights like his comic counterpart, mixing his different abilities to great effect. Bonus points for their third encounter and Peter not stopping his talking.
During the fight at the school, the Lizard throws Peter through a wall, then creates an explosive out of nearby scientific equipment and throws it in after Peter. It shows the Lizard isn't just some mindless beast.
During the fight in the school, Peter is getting his ass handed to him, until he decides to stop fighting like a man - and starts fighting like a spider. He then webs the Lizard thoroughly, even crawling around his body like an actual spider, until the damn thing is cocooned and strung up.
Peter going to Capt. Stacey when he finds out that Connors is the Lizard. And the fact that he put it together at all; usually in comic books or movies characters really have to have the obvious spelled out for them, so props to Peter for figuring it out and jump to the reasonable response.
Gwen refusing to leave Oscorp before the antidote has finished production.
Gwen improvising a flamethrower to ward off the Lizard as well as using a flame to set off the smoke detector and fog up the room. She never loses her head, even when facing a foe that she knows she can't kill. Like the train passengers and Doc Ock in Spider-Man 2, this is a moment for both the civilian and the villain at once. The Lizard's reaction to the flamethrower is to pretty much shrug it off and embrace the flames, showing that not even being set on fire can stop him.
In a more meta sense, the fact that we finally have a Spider-Man movie where the female lead kicks some ass. To Mary Jane's credit in the original trilogy though, she did hit Venom on the head with a concrete block, but did so while being held hostage. Gwen, despite knowing the danger, follows Spidey and the Lizard through the school and saves Peter by attacking a massive, super-strong monster.
the S-02; a city-wide battle with a gigantic burrowing snake robot.
The S-03; Spidey and Lizard fighting side-by-side.
Gwen repairing a broken down Hunter enough to aid Spidey in a fight against a swarm of the mutated people with the usage of Frickin' Laser Beams! That's right, Peter and Gwen actually fight side-by-side!
Heck, just before that, one of the mutants tries climbing up on the Hunter to get at Gwen...and she punches it so hard it falls down!
Any of the Hunters, with Spider-Man actually chasing them!
Simply the fact that Beenox had the balls to write the Lizard as a hero. It certainly would have been surprising to a lot of people to see the Lizard freak saving them, when a few months before, he was threatening the very same city.