Linux provides a suite of tools, isapnptools, that configure and initialize ISA PNP cards. These are useful for setting up things like modems and sound card that are Plug and Play. Indeed, these tools allow you to control every aspect of how the cards are set up if you choose. You don't have to worry about your programs no longer working if you add a new card to your computer.
Note that Linux has no problem with PCI Plug and Play cards.