That information is stored in the Launch Services database. The
lsregister command can be used to manipulate that database. As far as I've been able to gather, you can only unregister an entire application, not an association for a specific file type. You can do that with this command:
/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -u /Applications/<appname>.app
But note that there is an automatic process in OS X that searches the /Applications folder and registers the applications it finds there. So if you have an application that wants to open a certain file type, the association might get recreated even if you have unregistered the application.
Someone may have a better answer than this but hopefully this will be at least a little helpful.