Encrypted Instant Messenger

If you are currently using an Instant Messenger like LINE, Telegram, Viber, WhatsApp or plain SMS messages you should pick an alternative here.

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Complete Comparison

securechatguide.org - Guide to Choosing a Messenger.
securemessagingapps.com - Secure Messaging Apps Comparison.
thinkprivacy.io - Simple Secure Messaging Apps Comparison.

Worth Mentioning

Ricochet - Ricochet uses the Tor network to reach your contacts without relying on messaging servers. It creates a hidden service, which is used to rendezvous with your contacts without revealing your location or IP address. Experimental Danger Keep Tor up to date
RetroShare - An E2E encrypted instant messaging and voice/video call client. RetroShare supports both TOR and I2P.
XMPP federated clients with OMEMO support:

Monal (iOS, MacOS) - An XMPP client in active development.
Conversations (Android) - An open source Jabber/XMPP client for Android 4.4+ smartphones. Supports end-to-end encryption with either OMEMO or OpenPGP.
Gajim (FreeBSD, Linux, Windows) - An open source fully featured XMPP client.
List of OMEMO ready clients

Kontalk - A community-driven instant messaging network. Supports end-to-end encryption. Both client-to-server and server-to-server channels are fully encrypted.
Status - Experimental A free and open-source, peer-to-peer, encrypted instant messanger with support for DAPPs.

Related Information

Updating the Tor binary included with Ricochet

Currently there are no known vulnerabilities with Ricochet. The software is safe to use as long as you update the included Tor binary to the latest version.

Download the Tor Browser.
Run the Tor Browser installer or extract package for your platform. Windows (.exe), MacOSX (.dmg) and Linux (.tar.bz2).
Copy the Tor binary or create a symbolic link to it:

Windows: Copy the Tor binary included with the Tor Browser and overwrite the old one included with Ricochet.

Tor Browser binary: %HOMEPATH%\Desktop\Tor Browser\Browser\TorBrowser\Tor\tor.exe
Ricochet's included binary: %HOMEPATH%\Desktop\Ricochet\tor.exe

MacOSX: Assuming you copied the Tor Browser.app and Ricochet.app from their respective .dmg install media to /Applications:
Create a symbolic link to the Tor binary in Terminal. Ricochet will continue to use the up to date version of the Tor binary when you update the Tor Browser Bundle.

rm ~/Applications/Ricochet.app/Contents/MacOS/tor ln -s ~/Applications/Tor\ Browser.app/Contents/Resources/TorBrowser/Tor/tor \ ~/Applications/Ricochet.app/Contents/MacOS/tor

Linux: Assuming you extracted the Tor Browser Bundle and Ricochet tarball to your home directory:

rm ~/ricochet/tor ln -s ~/tor-browser_en-US/Browser/TorBrowser/Tor/tor ~/ricochet/tor