To cite the 'knitr' package in publications use:

Yihui Xie (2013). knitr: A general-purpose package for dynamic report generation in R. R package version 1.5.
Yihui Xie (2013) Dynamic Documents with R and knitr. Chapman and Hall/CRC. ISBN 978-1482203530
Yihui Xie (2013) knitr: A Comprehensive Tool for Reproducible Research in R. In Victoria Stodden, Friedrich Leisch and Roger D. Peng, editors, Implementing Reproducible Computational Research. Chapman and Hall/CRC. ISBN 978-1466561595

Corresponding BibTeX entries:

  @Manual{,
    title = {knitr: A general-purpose package for dynamic report
      generation in R},
    author = {Alastair Andrew and Alex Zvoleff and Brian Diggs and
      Cassio Pereira and Hadley Wickham and Heewon Jeon and Jeff Arnold
      and Jeremy Stephens and Jim Hester and Joe Cheng and Jonathan
      Keane and J.J. Allaire and Johan Toloe and Kohske Takahashi and
      Michel Kuhlmann and Nacho Caballero and Nick Salkowski and Noam
      Ross and Ramnath Vaidyanathan and Richard Cotton and Romain
      Francois and Sietse Brouwer and Simon de Bernard and Taiyun Wei
      and Thibaut Lamadon and Tom Torsney-Weir and Trevor Davis and
      Weicheng Zhu and Wush Wu and Yihui Xie},
    year = {2013},
    note = {R package version 1.5},
    url = {http://yihui.name/knitr/},
  }
  @Book{,
    title = {Dynamic Documents with {R} and knitr},
    author = {Yihui Xie},
    publisher = {Chapman and Hall/CRC},
    year = {2013},
    note = {ISBN 978-1482203530},
    url = {http://yihui.name/knitr/},
  }
  @InCollection{,
    booktitle = {Implementing Reproducible Computational Research},
    editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
    title = {knitr: A Comprehensive Tool for Reproducible Research in
      {R}},
    author = {Yihui Xie},
    publisher = {Chapman and Hall/CRC},
    year = {2013},
    note = {ISBN 978-1466561595},
    url = {http://www.crcpress.com/product/isbn/9781466561595},
  }