Q: Changing from El Capitan to Sierra

Yes.  PHP is updated to 5.6.  The primary thing I encountered was PHP 5.6 defaults to checking SSL certificate chains and peer names.  Apparently PHP 5.5 did not.  This resulted in Roundcube login failures.  Here's a thread to start with, http://www.roundcubeforum.net/index.php?topic=22035.0.  I am unable to get Apple's openssl 0.9.8zh to validate my certificate chain so far, so I ended up setting verify_peer_name => false until I can figure the SSL stuff out.  I believe this ends up being the same behavior as PHP 5.5.

You are using mysql, but I was using postgres.  The other problem I encountered is that Apple's new PHP 5.6 appears to have left off a compiler switch "--with-config-file-scan-dir=/Library/Server/Web/php/".  This results in the /Library/Server/Web/php/php.ini file not being loaded, as it was previously.  This file loaded the postgres drivers pdo_pgsql.so/pgsql.so, and thus PHP couldn't access my postgres databases anymore.  I had to copy the setting directly into the main php.ini file as a workaround.  There were a couple other settings in the server php.ini as well, so you may look in there to make sure those extra settings aren't important.

I've installed Sierra in one server test computer to check any problem because we use FileMaker Server 15 with his own web server and this was a conflict point in our last updates.

After Sierra update I've installed FileMaker Server but this cannot succeed because the 80 and 443 ports are occupied.

I've checked server app and the web server it's closed.

In terminal I can see how this ports are listen and it's impossible to close from terminal with this error message in it.

"/System/Library/LaunchDaemons/org.apache.httpd.plist: Could not find specified service"

At the end we can not use the last update of Filemaker Server 15.0.2 and Sierra update in our servers

PHP is fine. Sierra is not supported by MySQL. Don't go for Sierra before MySQL supports it. Or move MySqL to a different server.

/Poul

The web service server seems to load /etc/php.ini which is just fine. In order to avoid PHP 5.6 SSL connection problems I installed OPENSSL macports package which contains an up-to date root CA bundle located by default at /opt/local/etc/openssl/cert.pem. Then in /etc/php.ini at the very end I uncommented the openssl.cafile and pointed it to the mac ports openssl root CA bundle as follows openssl.cafile=/opt/local/etc/openssl/cert.pem . Further I uncommented the openssl.capath in php.ini and pointed it to the server's own certificate storage at /etc/certificates as follows openssl.capath=/etc/certificates.

By these adjustments the built in PHP was be able to validate either local server certificates and ordinary server certificates that common browsers usually validate. In my case this made roundcube working again. Further remember to adjust roundcube configs to use FQDN hostnames for IMAP/SMTP connections  corresponding to the FQDN of your server certificate used for these services. By the way if you want to check current PHP SSL verification paths just invoke php -r "print_r(openssl_get_cert_locations());"  in terminal.