Under Ubuntu systems I personally keep mine in /etc/apache2/ssl/private or similar httpd etc created area.
sudo mkdir /etc/apache2/ssl
sudo mkdir /etc/apache2/ssl/private
sudo chmod 755 /etc/apache2/ssl
sudo chmod 710 /etc/apache2/ssl/private
You can also use the group 'ssl-cert' for 'private/' under Ubuntu:
sudo chown -R root:root /etc/apache2/ssl/
sudo chown -R root:ssl-cert /etc/apache2/ssl/private/
(If you do not have ssl-cert group, just use root:root for everything under ssl/.)
Put needed public www ssl certificate(s) in /etc/apache2/ssl
Put needed private ssl key(s) in /etc/apache2/ssl/private
sudo chmod 755 /etc/apache2/ssl/*.crt
sudo chmod 640 /etc/apache2/ssl/private/*.key
Then edit any web server '.conf' files and where they point for SSL as needed.
Restart web service.
As mentioned, it really doesn't matter where you put your private key(s) as long as you properly protect them.