Some vendors provide binary (closed source) drivers for Linux, but it is not always necessary to use these drivers. By definition, a smartcard is a secure device and the software can not be changed at will. This software is rarely free software within the principles of the Debian Free Software Guidelines - however, the software on the Debian system is completely free. Smartcards have their own internal software and operating systems. However, GnuPG can also use regular PKCS#11 cards with the help of OpenSC and the GnuPG PKCS#11 project For the GnuPG use-case (signing email), they are easy to use and therefore quite popular - however, to use a card for general purpose activities such as web authentication, VPN and disk encryption, they may not be satisfactory.
OpenPGP cards are a special type of card that are designed for use with GnuPG. This page describes the PKCS#11 style cards. There are two main types of solution on Debian, the OpenPGP based cards or the PKCS#11 style cards. All cards, readers and software are not interchangeable.