There's BTC, and everything else. But how are the call letters registered and is there a comprehensive list of them all?
As said above, there's no real, official "standard" everybody follows. Now then, you can go have a look at different exchanges and see what the call them. Cryptsy is famous for allowing you to deal with dozens of crypto-currencies, and they're constantly adding new ones (as well as taking out those deemed defunct) - you could go to their home-page and download
Be warned, though, that not all call-signs are 3 letters-long, though. Dogecoin appears as "DOGE" in most of the exchanges it appears at, and forty-two-coin is usually represented as just "42".
Some call-signs, off Cryptsy's page - notice the 4-lettered ones, the non-obvious (as eMark being "DEM" or Primecoin being "XPM") and the potentially confuse (as "LK7" and "LKY")
42 42Coin ALF AlphaCoin AMC AmericanCoin ANC AnonCoin ASC AsicCoin BET Betacoin BQC BBQCoin BTC Bitcoin BTE ByteCoin BTG BitGem BUK CryptoBuck CAP BottleCaps CAT CatCoin CENT Pennies CGB CryptogenicBullion CMC Cosmoscoin CNC CHNCoin COL ColossusCoin CSC CasinoCoin DBL Doubloons DEM eMark DGC DigitalCoin DOGE Dogecoin DVC DevCoin EAC EarthCoin ELC ElaCoin ELP ElephantCoin EMD Emerald EZC EZCoin FFC FireflyCoin FLO FlorinCoin FRC FreiCoin FRK Franko FST FastCoin FTC FeatherCoin GDC GrandCoin GLC Globalcoin GLD GoldCoin GLX Galaxycoin GME GameCoin IFC InfiniteCoin IXC IXCoin KGC KrugerCoin LK7 Lucky7Coin LKY LuckyCoin LOT LottoCoin LTC LiteCoin MEC MegaCoin MEM MemeCoin MNC MinCoin NAN NanoToken NBL Nibble NEC NeoCoin NET Netcoin NMC NameCoin NRB NoirBits NVC NovaCoin PHS PhilosopherStone PPC Peercoin PTS ProtoShares PXC PhoenixCoin QRK Quark RED RedCoin RYC RoyalCoin SBC StableCoin SXC SexCoin TGC TigerCoin TRC TerraCoin UNO Unobtanium WDC WorldCoin XNC XenCoin XPM PrimeCoin YBC YBCoin ZET ZetaCoin
I don't think you'll find a complete list since there are so many of them out there. Some alt coins have changed their 3 character codes, some alt coins have used the same 3 character codes that had been used by a different coin in the past.
I've been keeping a list of my addresses on the spreadsheet below but this spreadsheet also lists a good number of alt coins.
The 3-call letters aren't standardized, all the alt coins are just modified protocols of the original Bitcoin protocol where differences can be as small as a different port. The 3-letters thing are just abbreviations people commonly use.