By default, when taking a screen capture of an entire window on OS X, a shadow will be added to the backdrop of the window.
This behavior can be disabled by running the following commands in terminal:
defaults write com.apple.screencapture disable-shadow -bool TRUE; killall SystemUIServer;
The first command changes the preference for shadows in screen captures.
The second kills SystemUIServer, which will make the changes take immediate effect.
If you want to revert the setting and add shadows to screenshots again, run the following command:
defaults write com.apple.screencapture disable-shadow -bool FALSE; killall SystemUIServer;