B of A - where I'm at currently, haven't had any problems. Like Tx said, I've heard of people experiencing difficulty when trying to resolve issues.
It depends on the amount of the check and the account, but usually they make ~30-40% of the deposited funds immediately available, but don't release the full amount until the check clears (usually a day or two). Can get kind of confusing in online banking when your deposits don't match up with the total - have to look at the pending transactions.
Wells fargo - My wife had her checking, savings, and ccard through them. During a few months last year we carried a large balance due to school and wedding expenses. At some point, Wells Fargo decided that she had signed up for auto-paying her ccard bill IN FULL from her checking account.
Of course, we didn't have the cash, so the payment didn't go through. The auto-pay KEPT TRYING every 8 hours or so for three days, until she signed in to her online banking just to check on things. Each time the auto pay didn't go through, they dinged us with account fees. Despite the fact that Wells Fargo could not tell us when, how, or who enrolled the auto pay, they refused to waive the account fees.
After badgering them on the phone, they eventually reduced the fees, but we still had to pay $90-ish for their mistake. Needless to say, the checking and savings accounts were closed and moved elsewhere. We're hanging on to the credit card only because it was her first line of credit ever and we don't want our score to get dinged.
Edit: Forgot about another Wells Fargo incident - One of their (at the time) brand-new envelopeless deposit machines ate a check my wife was depositing. Tore it in half inside the machine and only spit back half of it. Happened over the weekend, we contacted them first thing monday morning. They mysteriously never found the other half of the check, which is a little worrisome since that's the part with the account number and all. Not too big of a deal, but it was a hassle getting a new check written for us.