Most game systems don't animate the objects prior to being put into the game. They will use some form of mesh deformation in order to achieve the desired result. Take a look at GameDev.com's "Earth, Wind, Fire and Water" contest for a few different examples.

What it mostly comes down to is making sure your script can somehow identify an objects overall stiffness (perhaps using a skill), and its spring back. Then you apply a few different algorithms to it (there are a few choices on GameDev - I will look for the links again a bit later if needed), which take both of those factors into account. Most can be translated into c-script relatively easily. This than will dictate how far certain models will bend and sway with the wind force applied.

Another option is to use an invisible particle system and use those particles to be your wind force. This has a few advantages, as it is easier to represent calm areas on a level (behind buildings for example). Again though, it still requires a certain ammount of information to be stored within the meshes to be affected. Gets to be quite processor intensive though.