Firstly, ClickBank requires a separate account for every different URL. In other words, you can’t sell one product on http://www.firstsite.com and a second one on http://www.secondsite.com. You can sell a selection of products on one site though. Each account requires a setup fee too.
Secondly, until an account has paid out $100 three times on ClickBank, you can’t request payments by direct transfer to your bank account. This is a fairly serious (expensive) disadvantage to anyone without a US$ bank account. I would need to either set up a bank account that deals with US$ with my bank, which I would need to have regular monthly cheques in order to justify the expense, or pay a substantial cost each time I banked a cheque, say $20-30. Once these costs start accumulating for every new account set up, it would get fairly expensive. PayDotCom pays directly to your PayPal account, which can often be transferred to a bank account for no extra cost.
Now, I’m sure PayDotCom has disadvantages too, I just don’t know what they are yet. I’ve also added the PayDotCom widget to the blog which promotes popular products from both PayDotCom and ClickBank (see below for example).