In publications arising from the use of Wannier90 please cite

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

Other Wannier-related papers

We used to maintain a list of all the papers published using Wannier90. But there are now over 800 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.