With BrainWallet, you need to spend every bit of coin used as inputs, otherwise whatever you don't spend goes as fees.
Is this only applicable to offline transactions,
Ya, sorry ... when manually building a transaction through BrainWallet's Transactions page, it doesn't stop you or notify you that you are not spending the full amount from the inputs. Which, causes the unspent amount to go to the miner.
Is that why my BW transaction here http://blockchain.info/tx/54268b0051821f4b25e3e863214ddd1490b22dc154f6fbe6ed7eca334501dba8
Threw away 1 satoshi as a fee?