Does MtGox charge commission in USD or in BTC?
Mtgox charges the fee from whatever you're buying.

So if you buy 100 btc for however many USD, you'll buy the BTC, then you'll be charged 0.6% of your 100btc as fee.

If you buy 100 USD for however many BTC (i.e., sell some btc), you'll get your USD, and will be charged 0.6% of your 100USD as fee.

Edit: This is actually configurable. If you go to the mtgox settings page in your account, you can set the fee to be taken out either as above (default), or out of your USD balance always.