Well, I think that most people will call a web-based application a mashup if it makes use of another party’s API. PubFocus clearly makes use of the NCBI Entrez API, so I think it could be called a mashup by this definition.

The article mentions some other interfaces for PubMed data that might be called mashups in the same way because they use this API (though it could be argued that the ones that run on Java aren’t “web-based”, so it depends how loose you want to be with the definition of “mashup.”):

SLIM (http://pmi.nlm.nih.gov/slim/)
MedKit (http://metnetdb.gdcb.iastate.edu/medkit/)
PubMed Assistant (http://metnet.vrac.iastate.edu/browser/)
XplorMed (http://www.ogic.ca/projects/xplormed/)

I think you already know about GoPubMed (http://www.gopubmed.org/) and ClusterMed (http://clustermed.info/).

The article also mentions PubFinder (http://www.glycosciences.de/tools/PubFinder), but I haven’t been able to reach it today. I did reach its google cache, though: http://tinyurl.com/u3zev

Best always,

-David