eCart and Power Store work with paypal standard and paypal payments pro.
I havent used shipworks, so rally cant say how it works.
it seams to me that what you are asking is can shipworks integrate with paypal. that is a question for paypal.
Your friends over here at WebAssist! These Dreamweaver extensions will assist you in building unlimited, custom websites.
These out-of-the-box solutions provide you proven, tested applications that can be up and running now. Build a store, a gallery, or a web-based email solution.