Key papers that chart the development of MITgcm are:

Marshall, J., C. Hill, L. Perelman, and A. Adcroft, (1997)
Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean modeling
J. Geophysical Res., 102(C3), 5733-5752.

Marshall, J., A. Adcroft, C. Hill, L. Perelman, and C. Heisey, (1997)
A finite-volume, incompressible Navier Stokes model for studies of the ocean on parallel computers.
J. Geophysical Res., 102(C3), 5753-5766.

Adcroft, A.J., Hill, C.N. and J. Marshall, (1997)
Representation of topography by shaved cells in a height coordinate ocean model
Mon Wea Rev, vol 125, 2293-2315

Marshall, J., Jones, H. and C. Hill, (1998) 
Efficient ocean modeling using non-hydrostatic algorithms.
Journal of Marine Systems, 18, 115-134

Adcroft, A., Hill C. and J. Marshall: (1999)
A new treatment of the Coriolis terms in C-grid models at both high and low resolutions.
Mon. Wea. Rev. Vol 127, pages 1928-1936

Marotzke, J, Giering,R., Zhang, K.Q., Stammer,D., Hill,C., and T.Lee, (1999)
Construction of the adjoint MIT ocean general circulation model and application to Atlantic heat transport variability
J. Geophysical Res., 104(C12), 29,529-29,547.

Adcroft, A. and J-M. Campin, (2004)
Rescaled height coordinates for accurate representation of free-surface flows in ocean circulation models. Ocean Modeling, Vol. 7 (3-4): 269-284

Adcroft, A., J-M Campin, C. Hill and J. Marshall (2004) Implementation of an atmosphere-ocean general circulation model on the expanded spherical cube.  Mon. Wea. Rev., 132 (12), 2845-2863

Marshall, J. A. Adcroft, J-M Campin and C. Hill (2004)
Atmosphere-ocean modeling exploiting fluid isomorphisms.  Mon. Wea. Rev., 132 (12), 2882-2894

Campin, J-M., A Adcroft, C. Hill and J. Marshall (2004) Conservation of properties in a free surface model. Ocean Modelling, Vol 6, 221-244.

Hill, C., C. DeLuca, V. Balaji, M. Suarez, and A. da Silva, 2004: Architecture of the Earth System Modeling Framework. Computing in Science and Engineering, Volume 6, Number 1.

A list of published papers that make use of MITgcm can be found here.