Unlike most desktop notifiers that merely send you to Gmail's mobile interface on the web, the most recent update to a cool Mac app called Aura actually implements Quick Reply functionality so you can reply to messages, or add a new message to any thread—right from its notification banner.
This nifty little app can save you time when you need to fire off a one-line response. It supports Gmail and Google Apps accounts, it's fully native and optimized for OS X Yosemite and El Capitan.