For accessing remote computers (which the original query was about)
  something like ssh or secure telnet using smart card based keys
  for authentication would be more appropriate.

Of course what you really want is for the session to be secure all the way
to the card, not just to the terminal.  And since you can't use the PIN as
an encryption key, you need something like a diffie-hellman exchange.  And
since the terminal makes a perfect man-in-the-middle, you need to add some
more protocol and use something like EKE, SPEKE, or OKE.

We did all this and wrote a paper:

N. Itoi, T. Fukuzawa, and P. Honeyman, "Secure Internet Smartcards," August
2000. Java Card Workshop, Cannes (September 2000).

http://www.citi.umich.edu/projects/smartcard/scpapers.html
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Linux Smart Card Developers - M.U.S.C.L.E.
(Movement for the Use of Smart Cards in a Linux Environment)
http://www.linuxnet.com/smartcard/index.html
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