The recommended citations for MOLCAS are:

General citations:

Molcas 8.0: F. Aquilante, J. Autschbach, R. K. Carlson, L. F. Chibotaru, M. G. Delcey, L. De Vico, I. Fdez. Galván, N. Ferré, L. M. Frutos, L. Gagliardi, M. Garavelli, A. Giussani, C. E. Hoyer, G. Li Manni, H. Lischka, D. Ma, P. Å. Malmqvist, T. Müller, A. Nenov, M. Olivucci, T. B. Pedersen, D. Peng, F. Plasser, B. Pritchard, M. Reiher, I. Rivalta, I. Schapiro, J. Segarra‚ÄźMartí, M. Stenrup, D. G. Truhlar, L. Ungur, A. Valentini, S. Vancoillie, V. Veryazov, V. P. Vysotskiy, O. Weingart, F. Zapata, R. Lindh, MOLCAS 8: New Capabilities for Multiconfigurational Quantum Chemical Calculations across the Periodic Table Journal of Computational Chemistry, 37, 506-541, (2016)

Molcas 7.4: F. Aquilante, L. De Vico, N. Ferré, G. Ghigo, P.-Å. Malmqvist, P. Neogrády, T.B. Pedersen, M. Pitonak, M. Reiher, B.O. Roos, L. Serrano-Andrés, M. Urban, V. Veryazov, R. Lindh, MOLCAS 7: the next generation, Journal of Computational Chemistry, 31, 224-247, (2010)

Code development: V. Veryazov, P.-O. Widmark, L. Serrano-Andres, R. Lindh, B.O. Roos, MOLCAS as a development platform for quantum chemistry software, International journal of Quantum Chemistry, 100, 626-635 (2004).

Molcas 7: G. Karlström, R. Lindh, P.-Å. Malmqvist, B. O. Roos, U. Ryde, V. Veryazov, P.-O. Widmark, M. Cossi, B. Schimmelpfennig, P. Neogrády, L. Seijo, MOLCAS: a program package for computational chemistry, Computational Material Science, 28, 222-239 (2003).

Special features:

Selection of active space:
V. Veryazov, P.-Å. Malmqvist, B. O. Roos, How to select active space for multiconfigurational quantum chemistry? International Journal of Quantum Chemistry, 111, 3329-3338 (2011).

Parallel CASPT2:
S. Vancoillie, M. Delcey, R. Lindh, V. Vysotskiy, P.-Å. Malmqvist, V. Veryazov, Parallelization of a multiconfigurational perturbation theory,Journal of computational chemistry, 34, 1937-1948 (2013).

Relativistic exact decoupling:
Exact Decoupling of the Relativistic Fock Operator, D. Peng, M. Reiher, Theor. Chem. Acc. 131 1081 (2012)
D. Peng, M. Reiher, Local Relativistic Exact Decoupling, J. Chem. Phys. 136 244108 (2012)

Molecular dynamics in Molcas:
I. Schapiro, M. N. Ryazantsev, L. M. Frutos, N. Ferré, R. Lindh, M. Olivucci, The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin Are Modulated by Bond Length Alternation and HOOP Driven Electronic Effects, J. Am. Chem. Soc., 133 3354-3364, (2011)

Orbital-free density embedding:
F. Aquilante and T. A. Wesolowski, Self-consistency in Frozen-Density Embedding Theory based calculations, J. Chem. Phys. 135 (2011) 084120

New gradient codes:
J. Boström, F. Aquilante, T. B. Pedersen and R. Lindh, Analytical gradients of Hartree-Fock exchange with density fitting approximations, J. Chem. Theory Comp. 9 (2013) 204212
J. Boström, V. Veryazov, F. Aquilante, T. B. Pedersen and R. Lindh, Analytical gradients of the second-order Moller-Plesset energy using Cholesky decompositions, Int. J. Quantum Chem. 114 321-327 (2014)
L. Freitag, M. Delcey, F. Aquilante, T. B. Pedersen, R. Lindh and L. Gonzalez, Analytical gradients of complete active space self-consistent field energies using Cholesky decomposition: Geometry optimization and spin-state energetics of a ruthenium nitrosyl complex, J. Chem. Phys. 140 (2014) 174103

F. Aquilante, T. Todorova, T. B. Pedersen, L. Gagliardi and B. O. Roos, Systematic truncation of the virtual space in multiconfigurational perturbation theory, J. Chem. Phys. 131 (2009) 34113

SplitCAS method:
G. Li Manni, F. Aquilante and L. Gagliardi, Strong Correlation Treated Via Effective Hamiltonians and Perturbation Theory, J. Chem. Phys., 134, 034114, (2011)

D. Ma, G. Li Manni and L. Gagliardi, The Generalized Active Space Concept in Multiconfigurational Self-Consistent Field Methods, J. Chem. Phys., 135, 044128, 2011

Constrained optimization using Z-matrix formalism:
V. P. Vysotskiy, J. Boström, V. Veryazov, A new module for constrained multi-fragment geometry optimization in internal coordinates implemented in the MOLCAS package, J. Comp. Chem. 34, 2657-2665 (2013)

Fragment method:
T. Tsuchiya, K. Shrestha, E. Jakubikova, Orbital Analysis and Excited-State Calculations in an Energy-Based Fragmentation Method, JCTC, 2013, 9, 3350-3363 (2013)