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In some cases yes. When I researched smart cards a few years ago there were portable programmers for cards containing a 16f84 microcontroller (in pirate satellite TV circles they are often called "gold cards" or "wafer cards") which copied the PIC firmware and eeprom data from one card to another.
Some smartcards are ASIC's and cannot be programmed. The functionality is all done with transistors, there is no software running on the
card and the write fuse for the data is blown at the factory.
Smartcards that let you change data on the card through the normal communications can obviously
be used without a PC. you can put phonenumbers on the SIM in a mobile phone without a PC>