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The R2008b release of MATLAB for the first time includes native support for netCDF. NetCDF support in R2008b manifests itself in the form of a package and it will utilize the netCDF-3 API. This will look quite a bit different than mexnc in its current form, so the obviously question is "Will my current netCDF MATLAB code run on R2008b?" The answer to that is, hopefully, yes, it should just work.
Please note that neither SNCTOOLS nor MEXNC nor the netcdf toolbox are supported by the MathWorks, so please do not ask the MathWorks for support regarding them. Also note that I did not write the netcdf toolbox, so I cannot give any support to it. If you have questions about SNCTOOLS or MEXNC, please continue to use the contact email address listed on this site, john.g.evans.ne@gmail.com.
MEXNC is an interface to NetCDF files for MATLAB, and has roughly a one-to-one equivalence with the C API for NetCDF. In fact, there's no better introduction to MEXNC than to read the NetCDF Documentation provided by Unidata. Here's a general overview of mexnc.
MEXNC currently has two backends. The new backend is MATLAB's native netcdf package, which used by default if mexnc detects MATLAB version R2008b or higher. The other backend is the original "mexnc mex-file", which is usually only used when the version of MATLAB is R2008a or below, but there are a couple of other situations where it can be used.
SNCTOOLS is a set of MATLAB programs that read and write netCDF files. It was originally written to use mexnc, but now it also has backends for the native MATLAB netcdf package as well as a java backend. Check the tutorial for some examples.
MEXCDF was the original name for the mex-file interface. Well, actually it used to be "mexcdf53". When the NetCDF-3 API was incorporated into the mex-file, it was suggested that "mexnc" would be a much less confusing name for the mex-file itself, and so a name change was instituted. MEXCDF remains as the umbrella name for this sourceforge site and all the m-file software related to the mex-file.