The Protocols (whitepapers)

Bitcoin: A Peer-to-Peer Electronic Cash System (Satoshi Nakamoto, Bitcoin’s inventor)
This is the key paper that started the whole crypto revolution. Even if you only understand 10% of it, you’ve got to read it. It’s like a rite of passage, and it will give you a context for what has happened since this paper was published in 2008.

A Next Generation Smart Contract & Decentralized Application Platform (Vitalik Buterin, Ethereum’s creator)
Arguably, this might be the second most important paper, after Nakamoto’s. Unsatisfied with the original Bitcoin premise, Vitalik Buterin set the bar higher on what cryptography can do to computer science and decentralized applications, and he painted a compelling vision in this seminal paper. Ethereum aims for the lofty goal of becoming “the world computer” by providing an ecosystem on which developers can create decentralized applications for the internet of value.

Ethereum Design Rationale
Ethereum runs it’s own wiki, and this page outlines the design rationale behind their implementation decisions.

Ethereum: A Secure Decentralized Generalized Transaction Ledger (Gavin Wood, Ethereum’s co-founder)
A technical paper that takes deeper dives at describing how Ethereum will build and deliver their technology.

Enabling Blockchain Innovations with Pegged Sidechains (Blockstream team)
There are high expectations around sidechains, another key concept that’s supposed to drive innovation around the Bitcoin blockchain, without disturbing its core principles. This paper was authored by nine notable authors and proposes a solution that enables bitcoins and other ledger assets to be transferred between multiple blockchains. Also, see this “Simple Explanation of Bitcoin Sidechains for a less technical interpretation to the same paper.

Ripple (Ripple Labs)
Ripple is a payment protocol that supports both fiat and cryptocurrency, and allows transactions to be settled without the need for a centralized clearing house. They focus on providing the infrastructure for cross-border payments

MultiChain Private Blockchain
This whitepaper written by Dr Gideon Greenspan was among the first to realize the potential of private (permissioned) blockchain for use in financial institutions. This paper argues some of Bitcoin’s shortcomings and introduces MultiChain as an off-the-shelf platform for the creation and deployment of private blockchains.

NXT is attempting to build an ecosystem based on its own blockchain, and focused on trustless financial transactions. It includes its own (computing) client and online wallets.

Tendermint (Jae Kwon)
Tendermint is a decentralized  consensus engine that runs on its own blockchain.

Factom provides “Proof of Existence” for any form of digital document by first reducing them to a 32byte hash. Then by adding that hash to the Bitcoin blockchain proves the existence of that document at a known point in time. This whitepaper then extends that idea. Each Factom subsystem in the group provides a “Proof of Process.” Proof of each step in a process can be entered into a “Factom chain” of provable events.

Permacoin: Repurposing Bitcoin Work for Data Preservation (Miller, Juels, Shi, Parno, Katz) A proposal that repurposes Bitcoin mining resources to achieve distributed storage of archival data.

Colored Coins: here are 2 papers to understand this concept, Overview of Colored Coins (Meni Rosenfeld, 2012), and this one.