Adding a self-signed certificate to the "trusted list"

The simple answer to this is that pretty much each application will handle it differently.

Also OpenSSL and GNUTLS (the most widely used certificate processing libraries used to handle signed certificates) behave differently in their treatment of certs which also complicates the issue. Also operating systems utilize different mechanisms to utilize "root CA" used by most websites.

That aside, giving Debian as an example. Install the ca-certificates package:

apt-get install ca-certificates

You then copy the public half of your untrusted CA certificate (the one you use to sign your CSR) into the CA certificate directory (as root):

cp cacert.pem /usr/share/ca-certificates

And get it to rebuild the directory with your certificate included, run as root:

dpkg-reconfigure ca-certificates

and select the ask option, scroll to your certificate, mark it for inclusion and select ok.

Most browsers use their own CA database, and so tools like certutil have to be used to modify their contents (on Debian that is provided by the libnss3-tools package). For example, with Chrome you run something along the lines of:

certutil -d sql:$HOME/.pki/nssdb -A -t "C,," -n "My Homemade CA" -i /path/to/CA/cert.file

Firefox will allow you to browse to the certificate on disk, recognize it a certificate file and then allow you to import it to Root CA list.

Most other commands such as curl take command line switches you can use to point at your CA,

 curl --cacert  /path/to/CA/cert.file https://...

or drop the SSL validation altogether

 curl --insecure https://...

The rest will need individual investigation if the ca-certificates like trick does not sort it for that particular application.

Non Interactive Approach

For use in a non-interactive context (e.g. a chef recipe) you can use the following sequence.

sudo cp my.crt /usr/local/share/ca-certificates/
sudo update-ca-certificates

• Tested and works on debian 5/6 & Ubuntu 14.04.
• For more information, see man update-ca-certificates

This method is preferred over @Drav's method, since /usr/share/ is typically reserved for files added by the OS / apt-get.

On Fedora 23, add the .pem or .der file to /etc/pki/ca-trust/source/anchors/ and run sudo update-ca-trust extract.

See man update-ca-trust for details, e.g. whether to use /etc or /usr.