Won't you get destroyed in fees doing this?

Which is more, paying x% on 1BTC of x% a hundred times on 0.01BTC?

I'm not familiar with the cost structure, but if there were a per-transaction cost then it would be:

which is more, paying x% + y once on 1 BTC or paying x% + y a hundred times on 0.01 BTC?

Clearly the latter is more, assuming of course that `y` is positive (and it would be a very strange market that inverted the structure)

Mt. Gox I believe has a flat percentage fee on all trades so someone can make as many micro trades as they want and still pay the same fee as one large trade.

It's pretty easy to solve by charging users who make over a certain limit of micro trades. I wonder why they haven't done this?

This actually seems like a large flaw in their fee structure. Every traditional online brokerage/trading service that I have looked at in the past has used a flat fee. This incentives individuals to reduce their number of transactions in order to limit the overall fee's paid.

On Bitfloor, you actually get up to 0.1% rebate on limit orders. From the docs:

"Any order that is on the order book will receive a rebate when filled. Think of this as a negative fee (you actually get extra funds). This is done to provide an incentive for some traders to place their orders onto the order book for others to better understand market conditions."

Same thing happens on the equity markets, with the difference being pocketed by the exchanges (they'll pay .29 cents per share to liquidity providers and charge .30 to liquidity takers)