The Gumstix basix and connex are based around the Intel PXA255 processor. This CPU has four UARTs on board, each of which can drive a serial port -- albeit with different capabilities and under different circumstances.
GPIO, AF1, AF2, AF3 below refer to the mode for GPIO pins. These echo commands are configuring how the GPIO pin works. GPIO means the pin can be used for a general purpose but the other three "alternate functions" will instead tie the pin to an internal PXA255 function like a clock or UART. The alternate functions available are different from pin to pin. See table 4-1 in the PXA Developer's Guide to see what alternate functions are available for each GPIO.
The FFUART (for Full-Function UART) serves as the default Linux console on the Gumstix, and supports rates of up to 230kbaud. It is exposed on nearly all 60-pin expansion boards.
The Gumstix Linux kernel maps the FFUART to /dev/ttyS0.
Despite its name, the Gumstix does not use the FFUART as a "full-function" serial port by default: when used as the system console, hardware flow control is disabled.
On all of the boards which have USB, the FFUART CTS and RTS signals are currently used as part of the USB hardware. The RTS is used to tell the host that it's ready (cable plugged in), and the CTS is used to detect cable insertion.
The STUART (for STandard UART) is available as a general-purpose serial port in most Gumstix configurations. The STUART supports rates of up to 230kbaud.
Note that the GPSstix expansion board uses the STUART to communicate with the GPS module (without flow control according to the schematics, so RTS and CTS could be used for other things).
The HWUART (for HardWare UART) is available as a general-purpose serial port in some Gumstix configurations. The HWUART supports rates of up to 921kbaud.
Note: The verdex motherboard does not have HWUART. There are only 3 UARTs on a verdex.
The HWUART is exposed on the console-hw expansion board.
The HWUART can be routed to two different sets of pins. By default, it is routed to a set of pins shared with the BTUART (and connected to the Gumstix's Bluetooth module, if present). It can be routed to a different set, freeing up the HWUART and leaving the BTUART to control the Bluetooth module. However, this second set of pins is shared with the PCMCIA/CompactFlash interface, and thus cannot be used with expansion boards which have a CF card interface, or a network interface (including the wifistix). Currently, this includes all connex-only expansion boards.
The BTUART (for BlueTooth UART) is not used in most Gumstix configurations, including those with Bluetooth (which is controlled by the HWUART by default). The BTUART supports rates of up to 921kbaud.
The BTUART is only available on newer expansion board with breakout pads (like breakout-gs, audiostix2, GPSstix). Its pins (shared with the HWUART) are directly connected to the Bluetooth module, if present, and are only brought to the 60-pin connector to go to the daughtercards on newer gumstix, see this chart for details.
Older gumstix brought out JTAG signals instead. If you are using Bluetooth on the gumstix, then the BTUART will not be available for other use.
See Breakout for a diagram showing the locations of the UART signals on the breakout-gs board.