I have to say that jessie dist upgrades throw in more than the usual share of issues. Until i write this more coherantly heres what i encountered:
Apache
- the major headache here is the changes to virtual host config files
- the second headache for vhosts is that they radically overhauled the authentication mechanisms,and most people will require a new Require all directive
Theres a howto here for both of the above at https://www.linode.com/docs/security/upgrading/updating-virtual-host-settings-from-apache-2-2-to-apache-2-4
- if you are using fastcgi / php_fpm dont forget you need the non-contrib and free repos in sources.list
- for fastcgi youll also need the require all directive, see https://www.linode.com/docs/websites/apache/install-php-fpm-and-apache-on-debian-8
- if you are using letsencrypt there is now a proper package, see https://certbot.eff.org/#debianjessie-apache, which has its own cronjob
Mysql
- watch out for mysql strict issues if you upgrade to mysql 5.6. You can ether disable it, or check ALL your code for strict violations.