I have seen the wikipedia article which is a bit sketchy on the details. I would like to know, in addition to general principles of operation, some practical details like:
Are they limited to compiled native programs or they can be employed with Java/Dot Net etc?
You have to check with the manufacturer of the dongle on what languages they support. Usually for Windows OS a DLL is supplied that can talk to the dongle and any language that can call into a DLL can use the dongle.