Здравствуйте, Василий Литвиненко!

Они отличаются длиной волны в волокне. Цитирую wikipedia (к сожалению русского перевода там нет, так что по-английски):

100BASE-FX
100BASE-FX is a version of Fast Ethernet over optical fiber. It uses a 1300 nm near-infrared (NIR) light wavelength transmitted via two strands of multi-mode optical fiber, one for receive(RX) and the other for transmit(TX). Maximum length is 400 metres (1,310 ft) for half-duplex connections (to ensure collisions are detected) or 2 kilometres (6,600 ft) for full-duplex. 100BASE-FX uses the same 4B5B encoding and NRZI line code that 100BASE-TX does. 100BASE-FX should use SC, ST, or MIC connectors with SC being the preferred option.
100BASE-FX is not compatible with 10BASE-FL, the 10 MBit/s version over optical fiber.
100BASE-SX
100BASE-SX is a version of Fast Ethernet over optical fiber. It uses two strands of multi-mode optical fiber for receive and transmit. It is a lower cost alternative to using 100BASE-FX, because it uses short wavelength optics which are significantly less expensive than the long wavelength optics used in 100BASE-FX. 100BASE-SX can operate at distances up to 300 metres (980 ft).
100BASE-SX uses the same wavelength as 10BASE-FL, the 10 MBit/s version over optical fiber. Unlike 100BASE-FX, this allows 100BASE-SX to be backwards-compatible with 10BASE-FL.
Because of the shorter wavelength used (850 nm) and the shorter distance it can support, 100BASE-SX uses less expensive optical components (LEDs instead of lasers) which makes it an attractive option for those upgrading from 10BASE-FL and those who do not require long distances.
100BASE-BX
100BASE-BX is a version of Fast Ethernet over a single strand of optical fiber (unlike 100BASE-FX, which uses a pair of fibers). Single-mode fiber is used, along with a special multiplexer which splits the signal into transmit and receive wavelengths.

Приложение:
http://en.wikipedia.org/wiki/Fast_Ethernet#Fiber