If you want to send a fee with every transaction, you can run bitcoin with the -paytxfee= option; there isn't much reason to do that now, unless you're generating lots of very small (few-bitpenny) transactions. The Bitcoin Faucet is running with -paytxfee=0.01 because it DOES generate lots of very small transactions.
From the wiki:
0.01 BTC fee if sending any transaction less than 0.01 BTC. This is to help prevent DoS attacks against the network. Remember: fees are not network-enforced, so it's still possible to send these small transactions without the fee -- you just have to generate the blocks that contain them yourself (after modifying Bitcoin).
0.01 BTC fee per kilobyte of transaction, but:
If the blocksize (size of all transactions currently waiting to be included in a block) is less than 27 kB, transactions are free.
If the blocksize is more than 250 kB, transactions get increasingly more expensive as the blocksize approaches the limit of 500 kB. Sending a transaction when the blocksize is 400 kB will cost 5 times the normal amount; sending when it's 499 kB will cost 500x, etc.
Transactions within each fee tier are prioritized based on several factors. Most importantly, a transaction has more priority if the coins it is using have a lot of confirmations. Someone spamming the network will almost certainly be re-using the same coins, which will lower the priority of their transactions. Priority is also increased for transactions with more BTC, and reduced for transactions with more data.
If the blocksize is over 4kB, free transactions in the above rules are only allowed if the transaction's priority is above a certain level.