I doubt they'll be going away anytime soon, although the ports may not be present on all mobos. Oddly enough it's usually the lower-end models that have them, and the high-end, more expensive ones with all the
other features don't, despite the SuperI/O chip already containing all the logic; they just decided to save a few cents omitting the traces and headers

The standard peripherals you get on one are usually a parallel port, 2 serial ports, a floppy controller, PWMs for fans, ADCs (temperature sensors), and some GPIOs.
On the other hand since all the SuperI/O chips I've seen have been QFP, it wouldn't be too hard to solder to the pins and bring out those ports that were left unimplemented. They're either disabled via strapping options or in the BIOS, either way not that difficult to re-enable again. (Maybe you could make use of those GPIOs too; built-in AVR/PIC/etc. programmer?

)