To cite plink in publications use:

Jonathan P. Weeks (2010). plink: An R Package for Linking Mixed-Format Tests Using IRT-Based Methods. Journal of Statistical Software, 35(12), 1-33. URL http://www.jstatsoft.org/v35/i12/.

Corresponding BibTeX entry:

  @Article{,
    title = {{plink}: An {R} Package for Linking Mixed-Format Tests
      Using IRT-Based Methods},
    author = {Jonathan P. Weeks},
    journal = {Journal of Statistical Software},
    year = {2010},
    volume = {35},
    number = {12},
    pages = {1--33},
    url = {http://www.jstatsoft.org/v35/i12/},
  }