Here's a list of protocols and software that use or support the superfast, super secure Ed25519 public-key signature system from Daniel J. Bernstein, Niels Duif, Tanja Lange, Peter Schwabe, and Bo-Yin Yang.

Encrypted, deduplicated backup tool, runs on Linux, *BSD, OS X and Windows.

These steps describe a full disk (including /boot) encrypted setup on a non coreboot enabled system using the great grml live distro.

Sequoia is a cool new OpenPGP implementation.  It consists of several
crates, providing both a low-level and a high-level API for dealing
with OpenPGP data.
It is written in Rust

NeoPG is a modern replacement for GnuPG 2
NeoPG starts as an opinonated fork of GnuPG 2 to clean up the code and make it easier to develop.
We want to provide a stable and extensible API for application developers, too.
Eventually, we will add new ways to use OpenPGP that make it accessible and usable.

Abstract.
ElsieFour (LC4) is a low-tech cipher that can be computed by hand;
but unlike many historical ciphers, LC4 is designed to be hard to break. LC4 is intended for encrypted communication between humans only, and therefore it encrypts and decrypts plaintexts and ciphertexts consisting only of the English letters A through Z plus a few other characters. LC4 uses a nonce in addition to the secret key, and requires that different messages use unique nonces. LC4 performs authenticated encryption, and optional header data can be included in the authentication. This paper defines the LC4 encryption and decryption algorithms, analyzes LC4’s security, and describes a simple appliance for computing LC4 by hand.

An extended version called LS47 can be found on https://github.com/exaexa/ls47, which includes a 3D-printable model of the tiles.

Monocypher is an easy to use crypto library inspired by libsodium and TweetNaCl.

Cryptocat is free software with a simple mission: everyone should be able to chat with their friends in privacy.

   Open source. All Cryptocat software is published transparently.
   Encrypted by default. Every message is encrypted, always.
   Forward secure. Chats are safe even if your keys are stolen.
   Multiple devices. Devices receive messages even when offline.
   File sharing. Securely share files with friends.

Available for Windows, Linux and Mac.

Open source (MIT licensed), available for iOS, Android, Windows, OS X and Linux.

Protect emails, files, hard drives, server certificates and online accounts using cryptography. Your secret keys are always stored securely in the Nitrokey hardware and can't be stolen. The device is PIN-protected and is secured against hardware attacks. Backups protect against loss.