How to cite large projects
pick the latest entry on their publication list that roughly covers
  the project as a whole


This sounds like the best you can do in this situation. You should clarify that you are referring to the project as a whole, e.g., by writing: 


  ... as found by the CompCert project (e.g., Foo &amp; Bar, 2012; see also http://compcert.inria.fr)...


The "e.g." clarifies that this is an example publication. I like xLeitix' suggestion of citing the project website. 



In this particular instance, I notice that there are no publications after 2012, so it seems like the project is finished, is it? In such cases, people might have a capstone publication "The CompCert project: overview, lessons learned and the way forward" that you could cite - which of course won't help you if the project is still ongoing.



Finally, you could of course contact the project's principal investigators and ask them how they would like the project to be cited. It would be a good idea to put such a piece of information somewhere prominent on the project website.