NetCDF 4 supports compressed files. Even if your programme does not make use of this feature, you can compress the output using the nccopy command (of an HDF enabled NetCDF 4 build).
The "-d 1" option sets the compression level to 1, which is the lowest compression level. However, in practice, files often don't become much smaller using higher levels, but the compression/decompression takes much longer. The "-s" enables shuffling of variable data bytes before compression and improves the compression rate without costing much.
The compressed NetCDF files can be used with any programme using NetCDF 4 (HDF based), e.g., Ferret, in the same way as uncompressed files.
To compress all NetCDF files in one directory, use something like
The compression rate obviously depends on the data. For instance, the output size of the climate model EMAC often can be reduced by about 50 %.
See also the NetCDF FAQs.