MEXNC is a mex-file 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 User's Guide for C provided by Unidata. It currently compiles with NetCDF library versions 3 and higher, and if it is built with 3.6.0 or higher, you should get the benefit of Large File Support. Here's a general overview of mexnc.
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.
SNCTOOLS is a set of m-files that sits on top of MEXNC (and optionally, java) and strives to provide the user with a kinder, gentler interface. If you really like java and need only to READ (not write) netCDF files or OPeNDAP URLs, then you can use SNCTOOLS and dispense with the mex-file entirely (although you will probably still want the m-files that come along with MEXNC). In general, the philosophy behind SNCTOOLS is "just get the data, please. Here's a short tutorial of SNCTOOLS.
The NetCDF Toolbox is also available for download, but is completely unsupported. That means you are completely on your own if you decide to use it. Some old documentation for it can be found here.
The mex-file interface was originally written by Chuck Denham at the USGS Woods Hole Science Center in Woods Hole, Massachusetts. In the fall of 2004, I was asked to take over maintenance, and in doing so, I thought it might be a good idea to move the code permanently onto Sourceforge. Sourceforge provides a mailing list for mexcdf, so if you wish to be apprised of all the latest developments, please consider subscribing.