Figuring out received transaction fee [merchant, json-rpc, bitcoind]

Hello!

I'm trying to figure out how can I get the fee that was applied to a transaction that was received by my bitcoind client. I use the "new address for every transaction" approach, so all my clients send their bitcoin to unique addresses. Based on that I'm able to find the transaction id and this is where i'm stuck at the moment. I somehow need to find out what transaction fee was actually paid by the client.
The reason is that we request, say, 0.1 BTC to pay, but when validating the payment I see that we received 0.0999 instead. So I need to actually figure out if client has sent less BTC or the fee was applied. At this point I use getreceivedbyaddress to check if I received funds to the address and then via listtransactions I can find the transaction in question. After that I'm at a loss at this moment.

I know about the fee formula - although the information differs from place to place, so which should I use is a question too. But i'm puzzled about which RPC calls will give me the required information and how do calculate the fee. Or is there a call, that can give me the fee applied to the transaction? Or should I read the block information and somewhere there is the transaction fee information?

Thanks for the help in advance.