A short update to "how FT2232 connects to Cyclone III on BeMicro"
BeMicro uses no additional JTAG buffers between FT2232 and FPGA, but a 10k pull-down resistor at TCK (and 10 k pull-up anyway). Furthermore it has 4052 muxes for the four JTAG lines to utilize it for PS configuration and apparently a user connection to FPGA alternatively. But I don't see, if or how these options are supported by the software driver. They could be used through FTDI d2xx driver, however. In addition, NCONFIG, NSTATUS and CONFIG_DONE are connected to FT2232 pins.
So all-in-all, as a minimal solution, a FT2232 can act as configuration interface with no additional glue logic.