As far as I know, there are pros and cons of each...
For ClickBank, the good thing is that there are much more affiliate marketers there - as we can see in many Internet Marketing guides - most of them revolve around promoting ClickBank products - so if you have a product in ClickBank, then chances are, you're going to get more affiliates to promote for you - which may mean more cash for you as a merchant!
Also, I heard that the affiliate system in PayDotCom is not as good compared to ClickBank - this was what I've heard... I can't verify this statement though as I've not promoted anything in PayDotCom before...
However, ClickBank merchant fees are more expensive compared to PayDotCom - IF I'm not wrong, for every product they approve, you have to pay $49.95... However, for PayDotCom, all you need to pay is a one-time fee (which is about $20+ if I haven't remember wrongly) and you can put up as many products as you like - and it is instant approval... However, for ClickBank, you have to wait for 3 - 5 business days for the ClickBank product approval team to go through and verify whether the product adheres to a list of conditions they have...
Also, another downside for ClickBank is that, for every sale, they will deduct from the merchant $1 + 7.5% as ClickBank fees... However, for PayDotCom - the fees is much lower (I'm sorry I can't remember off hand how much exactly they'll deduct)...
If you are deciding where you want to put your product in - I would suggest you try submitting your product to ClickBank for approval first... If they do not approve your product, then you put it in PayDotCom...
Anyways it's just my own personal two-cents opinion... And hope you'll find it useful...
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