The closest modern thing to it is probably the Raspberry Pi GPIO header.

Your BeBox case was lovingly spray painted in a conference room with inadequate ventilation by us at Be at corporate HQ in Menlo Park. Each one was lovingly assembled by the actual people who designed the hardware and wrote the code.

The old school way to do I/O on desktop was via the parallel port, which I imagine would still work if you get a PCIe parallel port card. For a more modern way, the FT232H chip supports UART, SPI, I2C, JTAG and raw GPIO over USB, and there are break-out boards available.