A good summary of recent advances, including an overview of basics and nomenclature, can be found here:
http://ipcc-wg1.ucar.edu/wg1/Report/AR4WG1_Print_Ch08.pdf
If you're looking for individual peer-reviewed papers, they are too numerous to list them all -- there are entire journals devoted to climate modeling. But you can start with these:
* Alexeev, V.A., et al., 1998: Modelling of the present-day climate by the INM RAS atmospheric model “DNM GCM”. Institute of Numerical Mathematics, Moscow, Russia, 200 pp
* Allan, R.P., M.A. Ringer, J.A. Pamment, and A. Slingo, 2004: Simulation of the Earth’s radiation budget by the European Centre for Medium Range Weather Forecasts 40-year Reanalysis (ERA40). J. Geophys. Res.,109, D18107, doi:10.1029/2004JD004816.
* Bernie, D., S.J. Woolnough, J.M. Slingo, and E. Guilyardi, 2005: Modelling diurnal and intraseasonal variability of the ocean mixed layer. J. Clim.,15, 1190–1202.
* Bleck, R., 2002: An oceanic general circulation model framed in hybrid isopycnic-Cartesian coordinates. Ocean Modelling, 4, 55–88.
* Boyle, J.S., et al., 2005: Diagnosis of Community Atmospheric Model 2 (CAM2) in numerical weather forecast configuration at Atmospheric Radiation Measurement (ARM) sites. J. Geophys. Res., 110, doi:10.1029/2004JD005042.
* Brogniez, H., R. Roca, and L. Picon, 2005: Evaluation of the distribution of subtropical free tropospheric humidity in AMIP-2 simulations using METEOSAT water vapour channel data. Geophys. Res. Lett., 32, L19708,doi:10.1029/2005GL024341.
* Brovkin, V., et al., 2002: Carbon cycle, vegetation and climate dynamics in the Holocene: Experiments with the CLIMBER-2 model. Global Biogeochem. Cycles, 16(4), 1139, doi:10.1029/2001GB001662.
* Burke, E.J., S.J. Brown, and N. Christidis, 2006: Modelling the recent evolution of global drought and projections for the 21st century with the Hadley Centre climate model. J. Hydrometeorol., 7, 1113–1125.
* Chapman, W.L., and J. E. Walsh, 2007: Simulations of arctic temperature and pressure by global coupled models. J. Clim., 20, 609-632.
* Claussen, M., et al., 2002: Earth system models of intermediate complexity: closing the gap in the spectrum of climate system models. Clim. Dyn., 18, 579–586.
* Collins, M., S.F.B. Tett, and C. Cooper, 2001: The internal climate variability of HadCM3, a version of the Hadley Centre coupled model without flux adjustments. Clim. Dyn., 17, 61–81.
* Collins, W.D., et al., 2004: Description of the NCAR Community Atmosphere Model (CAM3.0). Technical Note TN-464+STR, National Center for Atmospheric Research, Boulder, CO, 214 pp.
* Collins, W.D., et al., 2006: The Community Climate System Model: CCSM3. J. Clim., 19, 2122–2143.
* Cox, P., 2001: Description of the “TRIFFID” Dynamic Global Vegetation Model. Technical Note 24, Hadley Centre, United Kingdom Meteorological Office, Bracknell, UK.
* Cramer, W., et al., 2001: Global response of terrestrial ecosystem structure and function to CO2 and climate change: results from six dynamic global vegetation models. Global Change Biol., 7, 357–373.
* Crucifix, M., et al., 2002: Climate evolution during the Holocene: A study with an Earth system model of intermediate complexity. Clim. Dyn., 19, 43–60, doi:10.10007/s00382-001-0208-6.
* CSMD (Climate System Modeling Division), 2005: An introduction to the first general operational climate model at the National Climate Center. Advances in Climate System Modeling, 1, National Climate Center, China Meteorological Administration, 14 pp
* Diansky, N.A., and E.M. Volodin, 2002: Simulation of the present-day climate with a coupled atmosphere-ocean general circulation model. Izv. Atmos. Ocean. Phys., 38, 732–747 (English translation).
* Driesschaert, E., 2005: Climate Change over the Next Millennia Using LOVECLIM, a New Earth System Model Including Polar Ice Sheets. PhD Thesis, Université Catholique de Louvain, Louvain-la-Neuve, Belgium, 214 pp, http://edoc.bib.ucl.ac.be:81/ETD-db/collection/available/BelnUcetd-10172005-185914/.
* Emori, S., A. Hasegawa, T. Suzuki, and K. Dairaku, 2005: Validation, parameterization dependence and future projection of daily precipitation simulated with an atmospheric GCM. Geophys. Res. Lett., 32, L06708,doi:10.1029/2004GL022306.
* Flato, G.M., 2005: The Third Generation Coupled Global Climate Model (CGCM3) (and included links to the description of the AGCM3 atmospheric model). http://www.cccma.bc.ec.gc.ca/models/cgcm3.shtml.
* Furevik, T., et al., 2003: Description and evaluation of the Bergen climate model: ARPEGE coupled with MICOM. Clim. Dyn., 21, 27–51.
* Galin, V. Ya., E.M. Volodin, and S.P. Smyshliaev, 2003: Atmospheric general circulation model of INM RAS with ozone dynamics. Russ. Meteorol. Hydrol., 5, 13–22.
* Gallée, H., et al., 1991: Simulation of the last glacial cycle by a coupled, sectorally averaged climate–ice sheet model. Part I: The climate model. J. Geophys. Res., 96, 13139–13161.
* GFDL GAMDT (The GFDL Global Atmospheric Model Development Team), 2004: The new GFDL global atmosphere and land model AM2-LM2: Evaluation with prescribed SST simulations. J. Clim., 17, 4641–4673.
* Gordon, H.B., et al., 2002: The CSIRO Mk3 Climate System Model. CSIRO Atmospheric Research Technical Paper No. 60, Commonwealth Scientific and Industrial Research Organisation Atmospheric Research, Aspendale, Victoria, Australia, 130 pp, http://www.cmar.csiro.au/e-print/open/gordon_2002a.pdf.
* Graham, R.J., et al., 2005: A performance comparison of coupled and uncoupled versions of the Met Office seasonal prediction general circulation model. Tellus, 57A, 320–339.
* Hargreaves, J.C., J.D. Annan, N.R. Edwards, and R. Marsh, 2004: An efficient climate forecasting method using an intermediate complexity Earth System Model and the ensemble Kalman filter. Clim. Dyn., 23, 745–760.
* Hourdin, F., et al., 2006: The LMDZ4 general circulation model: Climate performance and sensitivity to parameterized physics with emphasis on tropical convection. Clim. Dyn., 27, 787–813.
* Hovine, S., and T. Fichefet, 1994: A zonally averaged, three-basin ocean circulation model for climate studies. Clim. Dyn., 15, 1405–1413.
* Jin, X.Z., X.H. Zhang, and T.J. Zhou, 1999: Fundamental framework and experiments of the third generation of the IAP/LASG World Ocean General Circulation Model. Adv. Atmos. Sci., 16, 197–215.
* Johns, T.C., et al., 2006: The new Hadley Centre climate model HadGEM1: Evaluation of coupled simulations. J. Clim., 19, 1327–1353.
* Jones, C.D., et al., 2005: Systematic optimisation and climate simulation of FAMOUS, a fast version of HadCM3. Clim. Dyn., 25, 189–204.
* K-1 Model Developers, 2004: K-1 Coupled Model (MIROC) Description. K-1 Technical Report 1 [Hasumi, H., and S. Emori (eds.)]. Center for Climate System Research, University of Tokyo, Tokyo, Japan, 34 pp., http://www.ccsr.u-tokyo.ac.jp/kyosei/hasumi/MIROC/tech-repo.pdf.
* Kiehl, J.T., and P.R. Gent, 2004: The Community Climate System Model, Version 2. J. Clim., 17, 3666–3682.
* Kiehl, J.T., et al., 1998: The National Center for Atmospheric Research Community Climate Model: CCM3. J. Clim., 11, 1131–1149.
* Krinner, G., et al., 2005: A dynamic global vegetation model for studies of the coupled atmosphere-biosphere system. Global Biogeochem. Cycles, 19, GB1015, doi:10.1029/2003GB002199.
* Lambert, S.J., and G.J. Boer, 2001: CMIP1 evaluation and intercomparison of coupled climate models. Clim. Dyn., 17, 83–106.
* Marchal, O., T.F. Stocker, and F. Joos, 1998: A latitude-depth, circulation biogeochemical ocean model for paleoclimate studies. Tellus, 50B, 290–316.
* Marsland, S.J., et al., 2003: The Max-Planck-Institute global ocean/sea ice model with orthogonal curvilinear coordinates. Ocean Modelling, 5, 91–127.
* Marti, O., et al., 2005: The New IPSL Climate System Model: IPSL-CM4. Note du Pôle de Modélisation No. 26, Institut Pierre Simon Laplace des Sciences de l’Environnement Global, Paris, http://dods.ipsl.jussieu.fr/omamce/IPSLCM4/DocIPSLCM4/FILES/DocIPSLCM4.pdf.
* Martin, G.M., et al., 2006: The physical properties of the atmosphere in the new Hadley Centre Global Environmental Model, HadGEM1. Part I: Model description and global climatology. J. Clim., 19, 1274–1301.
* Maxwell, R.M., and N.L. Miller, 2005: Development of a coupled land surface and groundwater model. J. Hydrometeorol., 6, 233–247.
* McFarlane, N.A., G.J. Boer, J.-P. Blanchet, and M. Lazare, 1992: The Canadian Climate Centre second-generation general circulation model and its equilibrium climate. J. Clim., 5, 1013–1044.
* Montoya, M., et al., 2005: The Earth System Model of Intermediate Complexity CLIMBER-3a. Part I: Description and performance for present day conditions. Clim. Dyn., 25, 237–263, doi:10.1007/s00382-005-0044-1.
* Oleson, K.W., et al., 2004: Technical Description of the Community Land Model (CLM). NCAR Technical Note NCAR/TN-461+STR, National Center for Atmospheric Research, Boulder, CO, 173 pp.
* Petoukhov, V., et al., 2000: CLIMBER-2: A climate system model of intermediate complexity. Part I: Model description and performance for present climate. Clim. Dyn., 16, 1–17.
* Petoukhov, V., et al., 2005: EMIC Intercomparison Project (EMIP-CO2): Comparative analysis of EMIC simulations of current climate and equilibrium and transient responses to atmospheric CO2 doubling. Clim. Dyn., 25, 363–385, doi:10.1007/s00382-005-0042-3.
* Pope, V.D., M.L. Gallani, P.R. Rowntree, and R.A. Stratton, 2000: The impact of new physical parametrizations in the Hadley Centre climate model: HadAM3. Clim. Dyn., 16, 123–146.
* Power, S.B., and R. Colman, 2006: Multi-decadal predictability in a coupled GCM. Clim. Dyn., 26, 247–272.
* Roeckner, E., et al., 1996: The Atmospheric General Circulation Model ECHAM4: Model Description and Simulation of Present-Day Climate. MPI Report No. 218, Max-Planck-Institut für Meteorologie, Hamburg, Germany, 90 pp.
* Roeckner, E., et al., 2003: The Atmospheric General Circulation Model ECHAM5. Part I: Model Description. MPI Report 349, Max Planck Institute for Meteorology, Hamburg, Germany, 127 pp.
* Salas-Mélia, D., 2002: A global coupled sea ice-ocean model. Ocean Modelling, 4, 137–172.
* Schmidt, G.A., et al., 2006: Present day atmospheric simulations using GISS ModelE: Comparison to in-situ, satellite and reanalysis data. J. Clim., 19, 153–192, http://www.giss.nasa.gov/tools/modelE/.
* Shibata, K., et al., 1999: A simulation of troposphere, stratosphere and mesosphere with an MRI/JMA98 GCM. Papers in Meteorology and Geophysics, 50, 15–53.
* Sokolov, A.P., et al., 2005: The MIT Integrated Global System Model (IGSM), Version 2: Model Description And Baseline Evaluation. Report No. 124, Joint Program on the Science and Policy of Global Change, Massachusetts Institute of Technology, Cambridge, MA, http://web.mit.edu/globalchange/www/MITJPSPGC_Rpt124.pdf.
* Weaver, A.J., et al., 2001: The UVic Earth System Climate Model: Model description, climatology and application to past, present and future climates. Atmos.-Ocean, 39, 361–428.
* Yu, Y., Z. Zhang, and Y. Guo, 2004: Global coupled ocean-atmosphere general circulation models in LASG/IAP. Adv. Atmos. Sci., 21, 444–455.
* Yu, Y., R. Yu, X. Zhang, and H. Liu, 2002: A flexible global coupled climate model. Adv. Atmos. Sci., 19(1), 169–190.
* Yukimoto, S., and A. Noda, 2003: Improvements of the Meteorological Research Institute Global Ocean-Atmosphere Coupled GCM (MRIGCM2) and its Climate Sensitivity. CGER’s Supercomputing Activity Report, National Institute for Environmental Studies, Ibaraki, Japan.