If you're worried about a "fund account with tiny bitcoins" attack, you should charge users that fund accounts with gazillions of tiny transactions an "excess account activity fee." I've been thinking about writing code for ClearCoin that does that, but at least so far it doesn't make sense for me to spend time doing that.
And see: https://github.com/bitcoin/bitcoin/pull/285 for the current thinking on how to handle fees at sending time.