I plan to setup an online wallet system using bitcoind that allows users to create their own bitcoin wallets. If a user on my system sends funds from his wallet to someone else's then bitcoind creates a block that needs to be inserted into the blockchain. Do I (as the wallet operator) receive the transaction fee? If not how do I allocate a transaction to myself (the operator?)
You don't, and you can't. The transaction fee needs to go to the miner who processes the transaction, otherwise your transactions won't get processed. You can, of course, charge whatever fees you want for whatever services you offer, but these have nothing whatsoever to do with the transaction fee for Bitcoin transactions themselves.