I loved my BeBox, but what would be the modern equivalent of the GeekPort? I've been using esp32/nRF52/etc boards for uart/spi/i2c/i2s/pwm-type work... it feels like hardware hacking on a desktop is a lost art.
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.
The closest modern thing to it is probably the Raspberry Pi GPIO header.