Along the same lines as credit card finance charges, I simply refuse to banking fees.
It isn't that I don't think they are justified, it's that I think they are a tax on ignorance and it's less costly to avoid fee-inducing banking situations.
To that end, I just got a "collected funds fee" at the bank, and investigated it. Here's the skinny from my banker:
"Yes, there's a difference between collected and available balance and your analysis is correct. Depending on where the funds are drawn from and if they've been collected is the determining factor. Funds might be available but not collected from the maker bank which means a portion of what is available is technically a loan to the customer and the reason for the fee (I was able to reverse it). Some customers find a balance between savings and checking or attach a line of credit to the operating account as an option to avoid the repeated fee."
So if you deposit checks regularly, you're going to see three balances. "Balance", "Available Balance", and "Collected Balance".
If you want to make sure you get no fees, find the lessor of those three numbers, and treat that as your "fee-free balance".
It's a game of inches...