In the episode, Secret Invasion, after most of the Avengers have been defeated by the Super Skrulls, Thor shows up with the real Captain America and basically goes ape on nearly all the Super Skrulls.
In the episode, Ultron Unlimited, all the heroes are captured and replaced with duplicates, with Thor the last one. He is defeated after monumental effort from the fake Avengers. After he is saved by Captain America he becomes the only one really holding his own versus Ultron and almost by himself defeats all the fake Avengers. After the Vision releases Ultron's head from his body, it is Thor that hammers it clear off his shoulders. Did I mention Ultron's body in the episode was made of Adamantium?
In the episode, Live Kree or Die, The Avengers are stuck on the Kree homeworld and being chased by the massive Kree army. Thor decides to stay back and fight them all himself, and he wins. He later rejoins the Avengers while they attempt to break the shield of the Supreme Intelligence, a job they were failing at, and breaks the shield with one hammer throw.
The last episode, Avengers Assemble, had Galactus appear to devour Earth. Galactus is pretty much unstoppable, and start sucking the life out of the planet. Spider-Man asks Captain America why he is so calm as the world ends, and Captain America tells him that he "hears it". Spider-Man asks him to clarify and Captain continues "I hear the thunder." Next scene is lightening coming down and knocking back Galactus, followed by Thor flying in, landing Mjornir straight into the world devourers chest, causing him to fall to his knees. He has his badass speech, and ends with him and Iron Man knocking Galactus into the negative zone. Total badass.