How can you distinguish the source of Bitcoins? As reported on Tech Dirt here the address of where the bitcoins seized from SilkRoad are being stored has been identified here. 

This has resulted in many people making micro payments to the wallet and attaching their own messages, I assume for the fun of it. 

Can the original funds the FBI paid to their wallet still be distinguished from the total fund now in the wallet after the additional transactions from 3rd parties? I assume they kept a tally of how much they transferred in but for the purposes of evidence I imagine they would need to know the actual coins and not just an amount.
Whenever a payment is sent to an address, it is received as a distinct transaction output. It should be a trivial task for the FBI to label the output or outputs accordingly to know which were created in the confiscation of Silk-Road's funds.

On the other hand, there is no such thing as the "actual coins". Whenever bitcoins are transferred, the outputs that feed the transaction are destroyed and new transaction outputs are created.