The Pushbullet notification synchronization tool now lets users compose and send replies via five different messaging apps. Those apps would be WhatsApp, Telegram, Hangouts, Facebook Messenger, and Line. Pushbullet picked up text message reply support several months ago.
Four of those services should work like a charm, just install the messaging app of your choice on your phone along with Pushbullet on both your phone and your computer, and you're off to the races. The only exception is Hangouts, which requires a slightly goofy workaround:
To reply to Hangouts messages from your computer, you'll need to have the Android Wear app installed. You don't need to actually have a watch, nor even open the app. Just install the app and you're good to go.
Technically, yes, each of these services offer desktop or web clients to read, compose, and send your replies, but there's something to be said for the simplicity of having them all come in with a unified notification style without requiring that service to be open on your computer.