Some successful Prolog variants are based around XSB, which is a logic programming and deductive database system that has found several successful research and commercial applications. Within my field of research, it is amongst others used by MulVal, which is a vulnerability analysis language: http://people.cis.ksu.edu/~xou/mulval/
It is also used in other areas, as shown in http://xsb.sourceforge.net/research.html: "for psychiatric diagnosis, as well as for fault diagnosis in electronic circuits. FLORA has been widely used for the creation of Web agents, for applications in neuroscience, and for processing ontologies and meta-data. Probabilistic logic programs have been used to allow mined association rules to be used within an intensional database. Preference Logic Programs have been used to for data cleaning through the formalism of Preference Logic Grammars. These applications typically mix the use of the various logics with traditional Prolog programming techniques. XSB with tabled constraints has been used for workflow rules for clinical oncology."
IBM Watson uses prolog for natural language processing: http://www.cs.nmsu.edu/ALP/2011/03/natural-language-processing-with-prolog-in-the-ibm-watson-system/