From his summary:
Pipes likes to aggregate, transform, and filter data feeds within the cloud, and can produce a few kinds of renderings in your browser. Popfly likes to aggregate, transform, and filter data feeds from the cloud, and can produce arbitrary renderings in your browser. They’re complementary because Popfly can consume and render data feeds coming from Pipes.His comparison follows a piece on PopFly in Sunday's NY Times.
I think these mashup tools are important because they foreshadow the potential of "information integration." Information Integration is the study of combining and summarizing information from multiple sources, often involving text or semi-structured data. It is #2 on Hector Molina's priority list after "Beyond Search," see Erik's summary of his WSDM keynote.
Content aggregators and vertical search engines that get good at information integration will have a significant competitive advantage "mashing up" content from multiple sources to create new and useful value for users.