With the recent fuss over Stormpay and E-gold, a website owner has to look and decide what is a good way to collect some of the revenue from the website.
Paypal offers a lot of convenience, but there are still plenty of Paypal Sucks websites that would urge caution on unsuspecting website designers.
In the event of certain disputes with Paypal, be warned. Paypal has the right to sieze your money in their account, and CAN clear out any bank accounts that are linked to a paypal account.
So, if you do decide to use Paypal, you can set up two bank accounts. One that is directly linked to paypal, and one for your business. On a regular basis (monthly or weekly) transfer the money from Paypal account to yours, leaving nothing but coppers there.