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Link popularity is a more broadly used factor and is used by a number of search engines. It's based on numher of pages/sites linking, irrespective of their value.
Reputation, on the other hand, goes beyond those in concept and scope and takes into consideration theme-related factors, or topics, that are determined by analysis of linking patterns and structures. It's a technology that's patent pending, developed in conjunction with the University of Toronto in Canada.
Automatic Determination of the Reputation of a Web Page on a Specific Topic [library.utoronto.ca]
While use of the technology is available for licensing, there are concepts that can be applied in site architecture and scoring that relate to site themes and determination, and designation of sites as hubs and authorities. There's also been some recent discussion about the possibility of themed Page Rank, with some strong arguments made in favor.