To be on this list, a currency must have a market cap of at least $10 million, otherwise there would be too many.

Billon: A cryptocurrency that represents fiat currencies
Bitcoin (BTC or XBT)
: An informative web site by the Bitcoin founders and community.
Ripple (XRP): A contained ecosystem + currency for performing fast settlements; doesn’t rely on the same computing scheme as Bitcoin.
Ripple Explained: Wikipedia article
IO Coin - a next-generation coin and blockchain (will it fly?)

Litecoin (LTC): A pure alternative currency.
MakerDAO: A smart stable coin for smart contracts
Ether (ETH): A token to enable Ethereum transactions that also functions as a currency. 
DASH (DASH): A currency designed for instant payments, similar to cash. 
DogeCoin (DOGE)
Safecoin (MAID): Designed for paying for P2P storage and processing. 


EthereumWallet*2: By Kryptokit*3: A bare bones wallet
BitGo*3: Enterprise level, two-factor security for permissioned asset management.
Bitt*4: Wallets for Caribbean nation citizens. 
Case*4: Easy to use, multifactor wallet. 
Etherli*2: Multi-sig wallet for Ether
Fuzo*3: SIM-based access to cryptobanking services
Ledger*4: Hardwallet for Bitcoin
Lightwallet*3: Browser-based Ether wallet
MyEtherWallet*2: A Chrome browser extension wallet for Ether. 
Simplex*3: Wallet and exchange using credit cards to guard against fraud.
Stellar*3: Open-source distributed finance and transfer platform. 
Xapo*3: A Bitcoin wallet and Bitcoin debit card. 


BitFinex*5: A centralized marketplace for Bitcoin and Litecoin, provides margin, swaps, etc. Serious about security, most of their assets are offline - they only maintain a small percentage online for trading.
BitStamp*5: A centralized fast exchange for Bitcoin only.
Bittrex*5: USA-based, “next generation” exchange
BTC China*5: A full-service, large-scale Bitcoin exchange with wallets, mining, payments, cold storage, etc.
BTC-e*4: Allows trading of fiat and virtual currencies centered around Europe, Russia, Asia.
CEX*4: USD and EUR exchange with many currencies
CoinBase*5: Provides wallets, exchange, and ties to your bank account. Enables merchant payments and settlements, no day-trading.
Coinut*4: Bitcoin-based options for trading or hedging.
Cryptsy*4: Offers centralized trading of over 200 different cryptocurrencies.
Digix*3: Ethereum tokens tied to physical gold: redeemable and tradable. Other assets as well.
EtherEx*2, by ConsenSys: A fully decentralized, open source currency exchange. Ethereum subcurrencies only.
Etherx*3: Bare-bones Ether-based wallet and exchange.
Genesis*4: Institutional-strength trading for large trades.
ItBit*4: Regulated US exchange
Kraken*5: A well funded, large US/Canadian exchange for pro BTC traders. Also ETH.
Lykkex*2: A hybrid exchange for colored coins that centralizes bids and prices but lets people execute bilaterally and settle using blockchains. Colored coins allow trading of assets, like securities, titles, debt, etc.
Poloniex*4: Full-service US-based exchange for all major currencies
ShapeShift*4: Move Bitcoins or convert to Litecoins in seconds, without an account.

This is my bookmark for keeping an eye on the various currencies:

Payments, Transfers, & Settlements

Abra*3: Peer to peer payment
Align Commerce*3: B2B cross-border payments
BankChain*3: Clearing and settlement, trust, gold and precious metals management
BitNet*4: Enterprise-grade digital commerce platform
BitPay*4: Point of Sale solution for retailers
BitPesa*3: Bitcoin transfers to Africa
Bitx*3: Bitcoin transfers for emerging markets
Bold*3: Billing, payments, and tax handling for contractors
ChangeTip*3: Micropayments
Circle*3: Easy mobile transfers
Kleering*3: Mobile-based cash transfer
Melotic*3: Transfer cash via mobile around the world
PaySwarm*3: Micropayments for content. 
Ripple*4: An open-source protocol for international settlement of transfers (replaces central bank transfer, wire transfer, etc.)
SETL*3: Fast, high volume settlements using Blockchain
Shift Card*3: A pre-paid debit card based on Bitcoin.
Stellar*3: An open-source, distributed platform for money transfer everywhere.
Web Payments Community Group: Developing next-generation payments systems for the developing world.

Pegged Cryptocurrencies

Price-Stable Cryptocurrencies, a SmartCoin primer
SmartCoins - cryptocurrencies that are pegged to the dollar, euro, etc., to eliminate currency risk for smart contracts. 

Cool Demos

EthereumPyramid*4: Bet one ether and get three back, a Ponzi scheme to show how smart contracts can scale securely. Eventually, some people will lose their ETH.

Asset Management

ColoredCoins: An open-source protocol for tying real assets to Bitcoins.
Digital Asset Holdings*4: A very well funded alternative to managing and settling asset transactions in seconds
Blockai*3: Content storage and authentication.
TradeBlock*4: Tools for institutional asset management and trading


Hedgy*4: Smart contracts for OTC futures

Local Currencies

Coin: A web site dedicated to local currency
Colu*3: Make your own currency in seconds, manage it with their dashboard