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.