The main papers describing VBFNLO are:

VBFNLO: A parton level Monte Carlo for processes with electroweak bosons – Manual for Version 2.7.0
J. Baglio, J. Bellm, G. Bozzi, M. Brieg, F. Campanario, C. Englert, B. Feigl, J. Frank, T. Figy, F. Geyer, C. Hackstein, V. Hankele, B. Jäger, M. Kerner, M. Kubocz, L.D. Ninh, C. Oleari, S. Palmer, S. Plätzer, M. Rauch, R. Roth, H. Rzehak, F. Schissler, O. Schlimpert, M. Spannowsky, M. Worek, D. Zeppenfeld
arXiv:1107.4038

Release Note: VBFNLO 2.7.0
J. Baglio, J. Bellm, F. Campanario, B. Feigl, J. Frank, T. Figy, M. Kerner, L.D. Ninh, S. Palmer, M. Rauch, R. Roth, F. Schissler, O. Schlimpert, D. Zeppenfeld
arXiv:1404.3940

Release Note: VBFNLO-2.6.0
K. Arnold, J. Bellm, G. Bozzi, F. Campanario, C. Englert, B. Feigl, J. Frank, T. Figy, B. Jager, M. Kerner, M. Kubocz, C. Oleari, S. Palmer, M. Rauch, H. Rzehak, F. Schissler, O. Schlimpert, M. Spannowsky, D. Zeppenfeld
arXiv:1207.4975

VBFNLO: A parton level Monte Carlo for processes with electroweak bosons
K. Arnold, M. Bahr, G. Bozzi, F. Campanario, C. Englert, T. Figy, N. Greiner, C. Hackstein, V. Hankele, B. Jager, G. Klamke, M. Kubocz, C. Oleari, S. Platzer, S. Prestel, M. Worek, D. Zeppenfeld
Comput.Phys.Commun.180:1661-1670, 2009
arXiv:0811.4559

Among these, the CPC paper, the manual and the newest release note should always be cited while using VBFNLO.

Additionally, the original literature on which the specific process is based on should be cited as well. Relevant publications are printed in the header of the program output. A list of papers concerning parts of VBFNLO is collected below. PhD and diploma/master theses concerning parts of VBFNLO can be found here.

Next-to-leading order jet distributions for Higgs boson production via weak-boson fusion
T. Figy, C. Oleari, D. Zeppenfeld
Phys.Rev.D68:073005, 2003
arXiv:hep-ph/030610

Higgs Production via Weak Boson Fusion in the Standard Model and the MSSM
Terrance Figy, Sophy Palmer, Georg Weiglein
JHEP 1202:105, 2012
arXiv:1012.4789

Dominant next-to-leading order QCD corrections to Higgs plus three jet production in vector-boson fusion
Terrance Figy, Vera Hankele, Dieter Zeppenfeld
JHEP 0802:076, 2008
arXiv:0710.5621

Next-to-leading order QCD corrections to Higgs boson production in association with a photon via weak-boson fusion at the LHC
Ken Arnold, Terrance Figy, Barbara Jager, Dieter Zeppenfeld
JHEP 1008:088, 2010
arXiv:1006.4237

QCD corrections to electroweak l nu_l jj and l^+ l^- jj production
Carlo Oleari, Dieter Zeppenfeld
Phys.Rev.D69:093004, 2004
arXiv:hep-ph/0310156

Next-to-leading order QCD corrections to photon production via weak-boson fusion
Barbara Jager
Phys.Rev.D81:114016, 2010
arXiv:1004.0825

Next-to-leading order QCD corrections to W+W- production via vector-boson fusion
Barbara Jager, Carlo Oleari, Dieter Zeppenfeld
JHEP 0607:015, 2006
arXiv:hep-ph/0603177

Next-to-leading order QCD corrections to Z boson pair production via vector-boson fusion
Barbara Jager, Carlo Oleari, Dieter Zeppenfeld
Phys.Rev.D73:113006, 2006
arXiv:hep-ph/0604200

Next-to-leading order QCD corrections to W+Z and W-Z production via vector-boson fusion
G. Bozzi, B. Jager, C.Oleari, D.Zeppenfeld
Phys.Rev.D75:073004, 2007
arXiv:hep-ph/0701105

Next-to-leading order QCD corrections to W+W+jj and W-W-jj production via weak-boson fusion
B. Jager, C.Oleari, D.Zeppenfeld
Phys.Rev.D80:034022, 2009
arXiv:0907.0580

Observing Strongly Interacting Vector Boson Systems at the CERN Large Hadron Collider
C. Englert, B. Jager, M. Worek, D. Zeppenfeld
Phys.Rev.D80:035027, 2009
arXiv:0810.4861

QCD Corrections to Vector-Boson Fusion Processes in Warped Higgsless Models
C. Englert, B. Jager, D. Zeppenfeld
JHEP 0903:060, 2009
arXiv:0812.2564

QCD corrections to hadronic WWZ production with leptonic decays
V. Hankele, D. Zeppenfeld
Phys.Lett.B661:103-108, 2008
arXiv:0712.3544

QCD corrections to charged triple vector boson production with leptonic decay
F. Campanario, V. Hankele, C. Oleari, S. Prestel, D. Zeppenfeld
Phys.Rev.D78:094012, 2008
arXiv:0809.0790

NLO QCD corrections to W+W- gamma and Z Z gamma production with leptonic decays
G.Bozzi, F.Campanario, V.Hankele, D.Zeppenfeld
Phys.Rev.D81:094030, 2010
arXiv:0911.0438

NLO QCD corrections to $W^\pm Z\gamma$ production with leptonic decays
G. Bozzi, F. Campanario, M. Rauch, H. Rzehak, D. Zeppenfeld
Phys.Lett.B696:380-385, 2011
arXiv:1011.2206

$W\gamma\gamma$ production with leptonic decays at NLO QCD
G. Bozzi, F. Campanario, M. Rauch, D. Zeppenfeld
Phys.Rev.D83:114035, 2011
arXiv:1103.4613

$Z\gamma\gamma$ production with leptonic decays and triple photon production at NLO QCD
G. Bozzi, F. Campanario, M. Rauch, D. Zeppenfeld
Phys.Rev.D84:074028, 2011
arXiv:1107.3149

NLO-QCD corrections to $W\gamma j$ production
F. Campanario, C. Englert, M. Spannowsky, D. Zeppenfeld
Europhys.Lett.88:11001, 2009
arXiv:0908.1638

Precise predictions for (non-standard) $W\gamma j$ production
Francisco Campanario, Christoph Englert, Michael Spannowsky
Phys.Rev.D83:074009, 2011
arXiv:1010.1291

NLO QCD corrections to $WZj$ production with leptonic decays
F. Campanario, C. Englert, S. Kallweit, M. Spannowsky, D. Zeppenfeld
JHEP 1007:076, 2010
arXiv:1006.0390

QCD corrections to non-standard $WZj$ production with leptonic decays at the LHC
Francisco Campanario, Christoph Englert, Michael Spannowsky
Phys.Rev.D82:054015, 2010
arXiv:1006.3090

Precise predictions for $W\gamma\gamma$+jet production at hadron colliders
F. Campanario, C. Englert, M. Rauch, D. Zeppenfeld
Phys.Lett.B704:515, 2011
arXiv:1106.4009

Higgs + 2 jets via gluon fusion
V. Del Duca, W. Kilgore, C. Oleari, C. Schmidt, D. Zeppenfeld
Phys.Rev.Lett.87:122001, 2001
arXiv:hep-ph/0105129

Gluon-fusion contributions to Higgs plus two-jet production
V. Del Duca, W. Kilgore, C. Oleari, C. Schmidt, D. Zeppenfeld
Nucl.Phys.B616:367-399, 2001
arXiv:hep-ph/0108030

Monte Carlo studies of the jet activity in Higgs + 2 jet events
V. Del Duca, G. Klämke, M.L. Mangano, M. Moretti, F. Piccinini, R. Pittau, A.D. Polosa, D. Zeppenfeld
JHEP 0610:016, 2006
arXiv:hep-ph/0608158

Higgs plus two jet production via gluon fusion as a signal at the CERN LHC
G. Klamke, D. Zeppenfeld
JHEP 0704:052, 2007
arXiv:hep-ph/0703202

Gluon-fusion contributions to Phi + 2 Jet production
Francisco Campanario, Michael Kubocz, Dieter Zeppenfeld
Phys.Rev.D84:095025, 2011
arXiv:1011.3819

Towards pp → VVjj at NLO QCD: Bosonic contributions to triple vector boson production plus jet
Francisco Campanario
JHEP 111-:070, 2011
arXiv:1105.0920