If you visit a webpage with a self-signed certification you will usually see the following warning: There is a problem with this website's security certificate.
To avoid the messge you need to install the certificate into the Trusted Root Certification Authorities certificat store. This can be done very easily with executing the following command:
certmgr -add Certificate.cer -s -r localMachine root
The certmgr command line tool can be found in the Windows Driver Kit Version 7.1.0