We have to install the following:

x php5
x php5-cgi
x php5-cli: to execute php script.
php5-mod-json, because we need to work with Json in our php script.
sqlite3-cli,
x php5-mod-sqlite3,
php5-mod-pdo-sqlite, our database engine and the libraries to access it from php.
openssh-sftp-server: to provide an easy way to upload the scripts to the yun, using WINSCP or similar.
nano: my favorite Linux text editor.
php5-mod-curl: we need to execute curl command from php.
x zoneinfo-europe,
x zoneinfo-core: this is needed to obtain the correct date and time in php.
logrotate: we will generate a few logs, which will grow very fast, and we need to rotate them.
php5-mod-xml: to encode and decode utf8 strings.