debian/ubuntu php5 (>= 5.4.0~rc6-1) has introduced two new commands:
php5enmod and php5dismod
# install the extension
sudo apt-get install php5-mcrypt
# you can see that it's installed by the presence of the .ini file
cat /etc/php5/mods-available/mcrypt.ini
# enable it
sudo php5enmod mcrypt
# reload Apache to make use of the extension
sudo service apache2 reload