Remove _specific_ items from Finder Open With menu

You can for example open /Applications/calibre.app/Contents/Info.plist and remove entries from the CFBundleDocumentTypes array. To apply the changes, run sudo touch /Applications/calibre.app/ or /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -f /Applications/calibre.app/ and relaunch Finder.

If the application is signed, it invalidates the code signature. And since 10.8 some applications like TextEdit and Chess have crashed on launch if the Info.plist has been modified.

This might do the trick. Under ~/Library/Preferences you'll find a file called com.apple.LaunchServices.plist. This file lists the preferred applications to open with for the different formats.

Opening the file with an editor such as TextMate should let you edit the associations.

Never say never. You can do that (albeit manually from the command line) with a CLI called lsregister - /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister. It can be used to either register launchers or unregister there. -dump will show you all the present associations, and -unregister can be used to selectively remove.