Note that the transactions are chosen by the client you issue your getwork requests to. If you're mining in a pool, the pool chooses the transactions.

The key settings are in the main.h file. Look at MIN_TX_FEE and MIN_RELAY_TX_FEE.

To accept non-standard transactions, comment out these lines in main.cpp:

// Rather not work on nonstandard transactions (unless -testnet)
if (!fTestNet && !IsStandard())
    return error("AcceptToMemoryPool() : nonstandard transaction type")

Note that if you accept transactions with less than the normal transaction fees, you should connect to Luke Dash Jr.'s node to make sure you get such transactions, since most clients won't relay them to you. Add -addnode=173.242.112.53 to the command line you use to start your client.