In publications arising from the use of Wannier90 please cite

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]

Papers introducing MLWFs and their applications

Other Wannier-related papers

We used to maintain a list of all the papers published using Wannier90. But there are now close to 300 papers and new ones appear at the rate of 2-3 each week! So here is link to the citations of the CPC article from google scholar.