Here is a great, well researched, and thorough article on the subject. It is published on September 5, 2008 -- so some information may be out of date by the time you read this:
http://www.eganltd.com/index.php?option=com_myblog&show=Which-bank-should-I-choose-for-my-business-.html&Itemid=55Spoiler alert: Here is the bank the authors ultimately chose:
So ... what is the bottom line? We ended up choosing Commerce Bank, for several reasons - first, completely free real-time balance information. We also like that it's open 7 days a week (we opened our accounts on a Sunday afternoon), it's open late, and deposits made before 6 p.m. are available next day. Commerce, to us, just seems to think differently about banking, and we liked how they think. However, with the recent Commerce-TD Ameritrade merger, we have no idea how Commerce's thinking might change. Until then, we're sticking with the friendly red "C" man.
But the entire article is worth reading, and you might choose one of the other reviewed banks for different reasons.