Under Ubuntu systems I personally keep mine in /etc/apache2/ssl/private or similar httpd etc created area.
All of this owned by root:
sudo mkdir /etc/apache2/ssl
sudo mkdir /etc/apache2/ssl/private
sudo chmod 755 /etc/apache2/ssl
sudo chmod 710 /etc/apache2/ssl/private
Copy/Move public www ssl certificate(s) to /etc/apache2/ssl
Move private key(s) to /etc/apache2/ssl/private - then:
sudo chmod 755 /etc/apache2/ssl/*.crt
sudo chmod 640 /etc/apache2/ssl/private/*.key
then verify root:ssl-cert owns it all:
sudo chown -R root:ssl-cert /etc/apache2/ssl
(^ owner:group can also be "root:root" - apache/nginx reads as root anyway - you can also do away with any group privilege in this case (private folder = chmod 700 / key file = chmod 600) if you do)
As mentioned, it really doesn't matter where you put your private key(s) as long as you properly protect them.