This has come up in my graduate program as well (English at the University of Victoria, home to the Digital Humnities Summer Institute). Reception has been lukewarm, but I came across the Claremont Graudate University's interesting idea of requiring what they call "Language and Research Tools."
For the PhD in History, "the student must demonstrate proficiency in two foreign languages or in one foreign language and an approved research tool . . . . With the advisor’s approval, a PhD student may substitute the second language requirement with Digital Humanities or oral history."
See: http://www.cgu.edu/pages/8200.asp in the middle of the page.
The English PhD has similar language, although the 'research tool' option is limited to digital humanities. See http://www.cgu.edu/pages/8210.asp
The University of Guelph PhD in Literary Studies/Theatre Studies in English Writes that "In certain cases, students' research may require demonstrable competency in a non-written or technical language such as a programming language. The selection of the language(s) will be determined by the student in consultation with the dissertation advisor, and must be submitted for approval by the Graduate Studies Committee." there doesn't seem to be an accepted (or at least outlined) method for assessing a programming language. See: http://www.uoguelph.ca/registrar/calendars/graduate/current/gradprog/sets-phd.shtml
UC Santa Cruz has similar language on the website for the PhD in Film and Digital Media: http://film.ucsc.edu/phd_program/requirements
Thinking about this in relation to the above, it seems like there might be precedent in in History for considering various specializations (oral history, quantitative methods), as well as in Linguistics. Personally, I really like Claremont's research tools idea, given the justifications that have bee explicitly put forth for reasons why multiple languages are required, ie, to be useful in primary research settings.