In publications arising from the use of Wannier90 please cite

Wannier90 as a community code: new features and applications
Giovanni Pizzi, Valerio Vitale, Ryotaro Arita, Stefan Blügel, Frank Freimuth, Guillaume Géranton, Marco Gibertini, Dominik Gresch, Charles Johnson, Takashi Koretsune, Julen Ibañez-Azpiroz, Hyungjun Lee, Jae-Mo Lihm, Daniel Marchand, Antimo Marrazzo, Yuriy Mokrousov, Jamal I. Mustafa, Yoshiro Nohara, Yusuke Nomura, Lorenzo Paulatto, Samuel Poncé, Thomas Ponweiser, Junfeng Qiao, Florian Thöle, Stepan S. Tsirkin, Małgorzata Wierzbowska, Nicola Marzari, David Vanderbilt, Ivo Souza, Arash A. Mostofi, Jonathan R. Yates, arXiv:1907.09788 (2019) [arXiv]

If you are using v.2.x or earlier, please cite instead:

An updated version of wannier90: A tool for obtaining maximally-localised Wannier functions
AA Mostofi, JR Yates, G Pizzi, YS Lee, I Souza, D Vanderbilt, N Marzari
Comput. Phys. Commun. 185, 2309 (2014) [ONLINE JOURNAL]

Papers introducing MLWFs and their applications

  • Maximally localized Wannier functions: Theory and applications
    Nicola Marzari, Arash A. Mostofi, Jonathan R. Yates, Ivo Souza, David Vanderbilt, Rev. Mod. Phys. 84, 1419 (2012) [ONLINE JOURNAL]
  • Wannier90: A Tool for Obtaining Maximally-Localised Wannier Functions
    A. A. Mostofi, J. R. Yates, Y.-S. Lee, I. Souza, D. Vanderbilt and N. Marzari, Comput. Phys. Commun. 178, 685 (2008) [ONLINE JOURNAL]
  • Maximally localized generalized Wannier functions for composite energy bands
    N. Marzari and D. Vanderbilt, Phys. Rev. B 56, 12847 (1997) [ONLINE JOURNAL]
  • Maximally localized Wannier functions for entangled energy bands
    I. Souza, N. Marzari and D. Vanderbilt, Phys. Rev. B 65, 035109 (2002) [ONLINE JOURNAL]
  • Ab initio transport properties of nanostructures from maximally localized Wannier functions
    A. Calzolari, N. Marzari, I. Souza and M. B. Nardelli, Phys. Rev. B 69, 035108 (2004) [ONLINE JOURNAL]
  • Band structure and quantum conductance of nanostructures from maximally localized Wannier functions: The case of functionalized carbon nanotubes
    Y. S. Lee, M. B. Nardelli and N. Marzari, Phys. Rev. Lett. 95, 076804 (2005) [ONLINE JOURNAL]
  • Spectral and Fermi surface properties from Wannier interpolation
    J. R. Yates, X. Wang, D. Vanderbilt and I. Souza, Phys. Rev. B 75, 195121 (2007) [ONLINE JOURNAL]
  • BoltzWann: A code for the evaluation of thermoelectric and electronic transport properties with a maximally-localized Wannier functions basis
    G. Pizzi, D. Volja, B. Kozinsky, M. Fornari, N. Marzari, Comput. Phys. Commun. 185, 422 (2014) [ONLINE JOURNAL]

Other Wannier-related papers

We used to maintain a list of all the papers published using Wannier90. But there are now over 1000 papers and new ones appear at the rate of 2-3 each week! So here is link to the citations of the Comput. Phys. Commun. article from Google Scholar.