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.