The system I am on uses
/etc/ssl/certs for certificates and
/etc/ssl/private for keys. Protection on the
/etc/ssl/private directory is 710. Root owns the directory and the group can only access keys if it knows their name. Careful use of groups and permissions can provide finer grain access to the keys by non-root users.
EDIT: As @UtahJarhead pointed out SSH is not SSL(TLS). SSH doesn't normally have any issues about key placement as they are placed by the tools. Both methods can be used to secure access. SSL/TLS uses CA (Certficate Authority) signed certificates stored as specified above.
SSH uses unsigned certificates. The server's (host's) keys are stored in /etc/ssh and the key has 600 permission allowing only root read access. These are generated and installed when the daemon is installed . Client/user keys are stored in ~/ssh (aka $HOME/ssh) and all the standard tools will place them accordingly. When a public key is copied for passwordless access it also is stored in ~/ssh for the target user on the target system.