Pull requests VERY welcome!
AnoNet is a decentralized friend-to-friend network built using VPNs and software BGP routers. anoNet works by making it difficult to learn the identities of others on the network allowing them to anonymously host IPv4 and IPv6 services)
BitMessage is a P2P communications protocol used to send encrypted messages to another person or to many subscribers. It is decentralized and trustless, meaning that you need-not inherently trust any entities like root certificate authorities. See whitepaper
Commotion Wireless is an open-source communication tool that uses mobile phones, computers, and other wireless devices to create decentralized mesh networks.
The Cryptosphere is an openly federated and fully decentralized encrypted cloud storage and application platform based on the Git data model
The Drogulus (WIP) is a programmable peer-to-peer data store. It's an open, federated and decentralised system where the identity of users and provenance of data is ensured by cryptographically signing digital assets.
eDonkey network is a decentralized, mostly server-based, peer-to-peer file sharing network best suited to share big files among users, and to provide long term availability of files
Freenet is free software which lets you anonymously share files, browse and publish "freesites" (web sites accessible only through Freenet) and chat on forums, without fear of censorship. Freenet is decentralised to make it less vulnerable to attack, and if used in "darknet" mode, where users only connect to their friends, is very difficult to detect.
Freifunk is a non-commercial initiative for free decentraliced wireless mesh networks. Technically Freifunk firmwares are based on OpenWRT and OLSR or B.A.T.M.A.N.
GNUnet is GNU's framework for secure peer-to-peer networking that does not use any centralized or otherwise trusted services.
Grimwire is a browser OS which uses Web Workers for process isolation, and WebRTC for peer-to-peer communication.
Guifi is a european (especially spanish) large network with over 22000 active nodes. Uses wifi in both infrastructure and mesh mode. Over 25km of fiber as well so far.
I2P is an anonymizing network, offering a simple layer that identity-sensitive applications can use to securely communicate. All data is wrapped with several layers of encryption, and the network is both distributed and dynamic, with no trusted parties.
Kademlia is a distributed hash table for decentralized peer-to-peer computer networks
NameCoin is a decentralized naming system based on Bitcoin technology.
Nightweb connects your Android device or PC to an anonymous, peer-to-peer social network. You can write posts and share photos, and your followers will retrieve them using BitTorrent running over the I2P anonymous network. It is still experimental.
LibreVPN is a virtual mesh network using tinc plus configuration scripts that even let you build your own mesh VPN. It's also IPv6 enabled.
OpenNIC Project is an alternative DNS provider that is open and democratic.
Osiris is software for decentralized portal, managed and shared via P2P between members.
PeerCDN automatically serves a site's static resources (images, videos, and file downloads) over a peer-to-peer network made up of the visitors currently on the site.
PeerServer is a peer-to-peer client server using WebRTC, where your browser acts as a server for other browsers across WebRTC peer-to-peer data channels.
Phantom is (was?) a system for generic, decentralized, unstoppable internet anonymity
Project Byzantium - Ad-hoc wireless mesh networking for the zombie apocalypse. The goal of Project Byzantium is to develop a communication system by which users can connect to each other and share information in the absence of convenient access to the Internet. This is done by setting up an ad-hoc wireless mesh network that offers services which replace popular websites often used for this purpose, such as Twitter and IRC.
Project Meshnet aims to build a sustainable decentralized alternative internet. Used by Hyperboria and built on CJDNS.
Quick mesh project is an openwrt based mesh networking firmware. Can be installed on any openwrt supported system. Auto configures any needed connections, auto detects internet connections and aunounces them. Native IPv6 support with IPv4 tunnels for current networking support.
RetroShare is an open source, decentralised communication platform. It lets you chat and share with friends and family, with a web-of-trust to authenticate peers.
The Serval Project lets mobile phones make phone calls to each other peer-to-peer without a base station.
Syndie is an open source system for operating distributed forums offering a secure and consistent interface to various anonymous and non-anonymous content networks.
Tahoe-LAFS is a Free and Open cloud storage system. It distributes your data across multiple servers. Even if some of the servers fail or are taken over by an attacker, the entire filesystem continues to function correctly, preserving your privacy and security.
Tavern is a distributed, anonymous, unblockable network designed to ensure that no one is silenced, censored, or cut off from the rest of the world
Telehash a new encrypted P2P JSON-based protocol enabling developers to quickly build apps that are distributed and private (see v2 of the spec)
The FNF is the free network foundation: teaching how to build wireless community networks.
Tidepools is being developed within the Red Hook Mesh Network, for addressing local, social incentives for mesh use. An Open Source, Collaborative, Mobile Mapping & Social Hub, Reflecting Community Needs & Culture through Custom Apps, Time-based Maps, & Data Feeds.
Tonika is a (digital) social network, which (by design) restricts direct communication to pairs of users who are friends, possesses many of the security properties (privacy, anonymity, deniability, resilience to denial-of-service attacks, etc.) that human sociaties implement organically in daily life.
Tor protects you by bouncing your communications around a distributed network of relays run by volunteers all around the world: it prevents somebody watching your Internet connection from learning what sites you visit, and it prevents the sites you visit from learning your physical location.
Tox The goal of this project is to create a configuration free p2p skype replacement.
Tribler Aims to create a censorship-free Internet. Already deployed, used and incrementally improved for 8-years. Tribler uses an upcoming IETF Internet Standard for video streaming and is backward compatible with Bittorrent. Future aim is using smartphones to even bypass Internet kill switches. An early proof-of-principle Tribler-mobile is available on the Android Market. Key principle: 'the only way to take it down is to take The Internet down'. Overview paper.
Unhosted - also known as "serverless", "client-side", or "static" web apps, unhosted web apps do not send your user data to their server. Either you connect your own server at runtime, or your data stays within the browser.
Vole is a web-based social network that you use in your browser, without a central server. It's built on the power of Bittorrent, Go and Ember.js. Uses bittorrent sync.
ZeroTier One is an open source application that creates huge distributed Ethernet networks. It makes use of supernodes, but these run the same code as ordinary nodes and end-to-end encryption protects all unicast traffic. Semi-commercial with a freemium model.
BitCoin is a digital currency, a protocol, and a software that enables it. Decentralized crypto-currency
LiteCoin is a peer-to-peer Internet currency that enables instant payments to anyone in the world (was based on Bitcoin)
PeerCoin/PPCoin is the first known cryptocurrency based on an implementation of a combined proof-of-stake/proof-of-work system
See bitcointalk for a list of others.