https://bitcointaxes.info

• imports trade history from MtGox, Coinbase, Bitstamp, BTC-e, Cryptsy, Bitfinex, Bitfloor, CampBX, LocalBitcoins
• manual entry of trades
• import/add cost basis for coins owned in 2012 or earlier
• calculates short / long term capital gains
• uses First-In-First-Out, average costing or "specific identification" (e.g. Last-In-First-Out)
• exports data ready to enter on Schedule D Form 8949
• exports TurboTax and TaxACT import data
• multi-year support for traders before 2013
• multi-currency support for your tax country: USD, GBP, EUR, CAD, AUD
• calculates gains for alt-coin and cross-coin trading
• shows closing positions balances and cost basis for next year
• tax estimate calculations for US tax payers
• free version for unlimited BTC trades and premium for alt-coins/multi-year

Coming soon:

• support for UK, Canada, Australia, Germany tax rules
• current year gain and tax liabilities
• maintain purchase records from coin addresses
• mining income calculators

If you are doing your own taxes, it would make sense to treat bitcoins / alt-coins as capital assets. Although I have read some accountants are filing as a currency but more so they can maximize the amount of taxes paid, to ensure their clients do not underpay. However, if you only have short term gains, you will be paying the maximum anyway.