I had the unpleasant suprise today to realize my Shaarli instance (a simple PHP application) stopped working after installing updates on my Debian web server. I was getting a 200 valid response from the web server, but with a zero-byte response length.
When installing the available updates on my Debian testing server, both the nginx and php5-fpm packages were updated (to versions 1.6.2-5 and 5.6.4+dfsg-1 respectively). After spending quite some time trying to figure out if this was due to a change in Nginx or PHP-FPM, reviewing the different log and config files, I finally found the following Nginx bug report which itself linked to an Ubuntu bug report which contained the solution to this issue:
However after upgrading to 1.6.1, you need to update the include line to this: include fastcgi.conf;
Adding this line in the appropriate nginx config file in /etc/nginx/sites-available did the trick. A quick sudo /etc/init.d/nginx restart later and Shaarli was up and running again.