How to cite the content of a zip file?
Looks like what you are actually citing is the software (which happens to be zipped), not the zip file itself. Obviously, how to do this this depends on what citation style you are using.

The according to the APA style blog, 


  
  Use an individual’s name in the reference if he or she has proprietary rights to the program. In all other cases, create a
  reference as you would for unauthored works. 
  After the title, in brackets, provide a descriptor for the item. This helps the reader immensely. 
  If the software is available online, provide the URL rather than the publisher name and location
  


While the MLA Style Guide says


  To cite software, use the following form:
  
  
  Epi Info [computer program]. Version 3.2. Atlanta, GA: Centers for
  Disease Control and Prevention; 2004.  
  Intercooled STATA (for
  Windows) [computer program]. Version 7.0. College Station, TX:
  StataCorp; 2000.
  
  
  Software need not be cited in the reference list if it is mentioned
  only in passing or is available without charge via the Internet (eg,
  shareware or freeware).


Whichever citation style you are using should likewise have guidance posted for how to cite software.

Edited to add:

Similarly, you should be able to find citation information in your chosen citation style for "citing datasets". Some examples are given At the MSU library site as well as other library sites. The APA, for instance (according to the above link) gives


  Unpublished raw data from study, untitled work
  
  Basic form:  Author, F. N. (Year). [Description of study topic].
  Unpublished raw data.
  
  Example: Smith, J.A. (2006). [Personnel survey]. Unpublished raw data.


Further edited for second follow-up question:

The University of Oregon Library website gives some general guidelines for citing any sort of data source:


  Citation Elements
  
  To be most effective, a data citation should include at least the
  following elements. The utility of these elements will depend on the
  research discipline, source data center/repository, and data format.
  
  
  Responsible party (i.e., study PI, sample collector, government agency) 
  Name of table, map, or dataset with any applicable unique IDs
  Name of data center, repository, and/or publication 
  Analysis software, if required 
  Date accessed 
  URL and/or DOI/DOI link or other persistent link