I don't think Batman could take down Thor. The other avengers, I can see a way, but Thor's damn hard to beat.
This is why mixing comic mythologies is silly, imo. It's cool to talk about like we are now, but Thor should not be a part of the Avengers. It's just dumb. He's a god, for chrissakes. He is immortal, he is pretty much all powerful, and he can call on the host of Asgard, who, by the way, are all similar to Thor in power. Yet he's running around with a snarky billionaire in a mechanical suit, a guy whose experiment went wrong, and a dude who was frozen in the 50s.
I loved the movie and the comics are fun, but to me, you want real comics? You want somebody who's done it right and kept away from all that mixing and matching shit? Go with The Sandman by Neil Gaiman. Or Fables by Bill Willingham. Unless the writers have created an entire world in which humankind is mutating or evolving, like they did with X-Men, it is ridiculous start implanting new heroes into stories that have no continuity. But that's just me. I realize I may be in the minority.
I just feel like Batman, as a comic, is great because it isn't set in a world, for the most part, in which people are able to shoot lasers out of their asses and fly. He works in that environment. He doesn't work as well in an environment in which a guy in a cape who can fly, is bulletproof, can run so fast that he actually "turns back time", etc. etc. etc., exists.