Currently there are rules that require certain transactions (not all, only spammy ones) to carry a minimum fee before it is even relayed through the network. In 0.3.20 and 0.3.21 this minimum is 0.01, in 0.3.22 it is 0.0005, in 0.3.23 it is 0.0001. We're looking for better schemes that do not have such a fixed limit, but for now some spam prevention is necessary. The rules used for creating transactions are an overestimation based on which clients/rules are in use in the network - we don't want transactions that linger forever before being confirmed.
For example my friend and I both mine on my account and I regularly manually pay him (usually about 0.10 every time). So if I really modified the client, it's likely that my tx will be relayed and accepted by the network? I know they'll be low priority txs, but if they can be confirmed in reasonable time I'll accept it.