Phoebe facing down Carlos's skepticism and insisting on giving water to the desert creatures in "All Dried Up". Of course, her good intentions are entirely misguided, but it's the first time she really stands up for what she believes in.
Not to mention her gravity-defying slam dunk in "Gains Weight".
Although one of her more notable moments is when she defeats Garth Sinew in the Teacherathalon, which is no small feat considering he had a team of his own. Granted, his focus on building up his strength may have caused him to neglect his stamina—a trait Ms. Frizzle has in abundance. Maybe there is a second heart in her chest, hidden behind some kind of perception filter.
Any time the class sticks it to Janet. They're nice kids, but Janet manages to be so mean to them that she always asks for it.
One of these moments that mixes with Crowning Moment of Heartwarming is when Arnold takes off his helmet on Pluto to get her to come home with the otherscontext She refused to come home without her massive pile of space stuff she was taking as proof she'd been to space, even though it wouldn't fit on the bus.
Earlier in the same episode as that, after finding out the class's original field trip destination—a planetarium—was closed for the day, Janet begins bragging about how her teacher is better because she never makes these mistakes, leading to this exchange.
Arnold:(Cutting off Janet) Nobody is better than Ms. Frizzle. Janet: Oh, yeah? Prove it! Arnold: STOP THE BUS!! (Ms. Frizzle complies. Arnold storms to the front of the bus.) Ms. Frizzle: Yes, Arnold? Arnold: Isn't there... you know... someplace else you could take us? Ms. Frizzle: You mean another planetarium? Arnold: Well, sort of, but...bigger. Ms. Frizzle: Bigger? Arnold: You know, the..."Big One." Ms. Frizzle: Oh, Arnold! Why didn't I think of that?
She then proceeds to pull the main lever to turn the bus into a spaceship to go to space. Keep in mind this is Arnold we're talking about. He hates these field trips, yet this time he willingly gets himself into one to show up his Jerkass cousin.