To cite OMEGA please use the following:

OMEGA OpenEye, Cadence Molecular Sciences, Santa Fe, NM.

Hawkins, P.C.D.; Skillman, A.G.; Warren, G.L.; Ellingson, B.A.; Stahl, M.T. Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and the Cambridge Structural Database J. Chem. Inf. Model. 2010, 50, 572-584.