The ocean carbon-cycle model intercomparison project (OCMIP) published some very interesting papers on numerical ocean models, also with focus on physics:

http://ocmip5.ipsl.jussieu.fr/OCMIP/

http://ocmip5.ipsl.jussieu.fr/OCMIP/

Model intercomparison project is now ongoing!

http://pft.ees.hokudai.ac.jp/maremip/index.shtml

You may check out the following link

http://www-pcmdi.llnl.gov/projects/model_intercomparison.php

If you want nice explanations about the difference between model and their numerical formalism you can check S. Griffies books especially:

Griffies, Stephen M., 2005: Some ocean model fundamentals In Ocean Weather Forecasting: An Integrated View of Oceanography, Berlin, Germany, Springer, 19-74.

cheers

Although not an intercomparison activity as such, you can find good information on http://www.clivar.org/clivar-panels/omdp/core

The global ocean circulation models used to be intercompared  years ago, even when they were stand-alone, or uncoupled from the atmosphere. Now they are more often being intercompared as parts of coupled climate models or even higher level of aggregation called "earth system models." The Coupled Model Intercomparison Project (CMIP5) is now in its phase 5:  http://cmip-pcmdi.llnl.gov/cmip5/. See, for example, one of the most recent publications related to this project by  Deshayes et al, 2014,  J. Climate, 27, 3298–3317; doi: http://dx.doi.org/10.1175/JCLI-D-12-00700.1 They compared how a number of models performed in the northern North Atlantic. There is an extensive reference list of many ocean and climate models. Hope this may help.

Thanks to all of you for your valuable inputs. Your answers helped me quite a lot.

Inter-comparison of a number of ocean circulation models for the Baltic Sea was carried out in the project "Eutrophication-Maps" where, as an example, the Gulf of Finland was studied, for which there is a significant number of hydrographic data. The main results of the project are described in Myrberg, K., Ryabchenko, V., Isaev, A., Vankevich, R., Andrejev, O., Bendtsen, J., Erichsen, A., Funkquist, L., Inkala, A., Neelov, I., Rasmus, K., Rodriguez Medina, M., Raudsepp, U., Passenko, J., Söderkvist, J., Sokolov, A., Kuosa, H., Anderson, T. R., Lehmann, A. &Skogen, M. D. 2010: Validation of three-dimensional hydrodynamic models of the Gulf of Finland. Boreal Env. Res. 15: 453–479. .