USB came out it 1996. Peripherals stick around a long time.
You'll soon need adapters to use those peripherals for laptops and Surface type devices.
I've only seen the joystick port appear on sound cards, which themselves are pretty much dead, and the AT connector was all but extinct by the mid 1990s.
New motherboards seem to fall into two camps: Legacy ports of all flavours, or ridiculous numbers of USB 3.0 ports. I saw one recently with 12 USB3.0 connectors on the back.