One use for these is using a smart card to authenticate to a website. This technology employs mutual SSL authentication where a user is authenticated by using a certificate. Usually you only have one-sided SSL authentication, where the server tries to authenticate that it really is who it says it is (normal SSL, EV, etc.), but this can also be done from the client side, resulting in much stronger authentication.
The smart card is used to store the private key of the certificate on the smart card, thereby making it much more difficult for the private key to be duplicated. Also some smartcards offer support for PIN numbers when trying to use the stored private key, resulting in two-factor authentication (something you have, the smart card, and something you know, the PIN number).