As an example, here is a block with 6 transactions:
http://blockchain.info/block-index/128373/000000000000a6dade9423c6cebb7222fb3155e28e5600b35b6f54cd8a1228f5You'll notice in this transaction from that block:
http://blockchain.info/tx/da5423baae6eeefa3535a8fb05304214b556b9ceed699316a9dd84b00f685326That there is exactly 1 input valued at 30.12 BTC and exactly 2 outputs (30.06 BTC & 0.05 BTC) resulting in total outputs of 30.11 BTC.
The difference between the total inputs in the transaction, and the total outputs is 0.01 BTC. This is how you pay transaction fees. You just include more in your inputs than in your outputs.
The miner created this transaction, called a coinbase transaction, when they built that block:
http://blockchain.info/tx/c338a4bc83d859feec4f9fab9bea5d5cdfa6d80804d026649f9e08e28a1126f5You'll see it has no inputs. The protocol normally doesn't allow transactions where the total of the inputs is less than the total of the outputs. However, it does allow each block to have exactly one such transaction (called a coinbase transaction) to be created by the miner with zero inputs. The block subsidy as determined by the protocol at the time of this block was 50 BTC (now it is 25 BTC). The protocol allows the total of the coinbase transaction to be no larger than the sum of the block subsidy and the transaction fees. Since there is only that one transaction in this block that paid fees, the value of the outputs in this coinbase transaction is 50.01 BTC.