That should create opportunity for automated trading. Identify large orders and place small orders a de minimis amount ahead of them when the bid-offer spread is sufficiently large. If someone trades with your bid (offer), try to be the best offer (bid) to exit and make the spread. If the large order behind you starts trading, trade with it to lose 0.01.
I've traded these markets by hand before using relative value signals from other exchanges (e.g. buy on bitstamp if btc-e moves up and bitstamp hasn't yet). You can't really do pure arbitrages since it takes so long to move money around but if you can identify which market leads you can use that as a starting point for coming up with a fair price to trade around. I made money easily but gave up on trying to automate it since the volume is so low, bid-offer spreads are often tighter than 2*trading fees, you can't short-sell easily/cheaply, exchanges seem incompetent or downright crooked, laughably bad APIs, etc.
These markets are wildly inefficient though. For a home day-trader or hobbyist there's easy money to be made. It's absurd how slowly price discovery trickles from one market to another. Most modern markets don't even get mispriced by a penny for more than a few microseconds, but there are nickels, dimes, quarters and even dollars of mispricing to capture in BTC/USD markets clicking on the screen.
You could probably dominate with an algo, but how much can you really make in a market that trades 10s of millions in notional value a day? There are also way too many exceptional conditions to let it run even semi-unattended since the exchanges are too immature. Anyone who's capable of doing it can make more doing the same thing on a real market.
ETA: Exchanges in this space are really, really bad. Some don't even know about rounding errors when using floating point for prices. Or would you trust trading on a market that can't even match trades as an atomic event? http://www.reddit.com/r/Bitcoin/comments/1r4d6t/bitstamps_st...