We highly recommend sticking to standards wherever they materialize. This is the best way to design a modular system and you'll be able to replace hardware and software modules that don't satisfy you. Therefore sticking to the standards makes you independent of smart card or reader manufacturers. Please don't misunderstand this statement. Nothing is more important than a good and healthy relationship with your suppliers, but hardware and software interfaces should be defined according to standards, whenever they exist. The following list contains links to important smartcard related standards:
ISO7816 identification card standard from the International Organization for Standardization.
EMV 96 3.11, Europay MasterCard Visa specification for payment systems.
PC/SC Builds upon existing industry smart card standards - ISO7816 and EMV - and complements them by defining low-level device interfaces and device-independent application APIs as well as resource management, to allow multiple applications to share smart card devices attached to a system.