What peripherals and/or support devices do you need on the board? Do you need any I/O connections to additional circuitry?
The Bemicro is limited in that it only has some RAM and a USB-to-RS232 UART as peripherals. You can add an 8-pin SPI FLASH device to the board (make sure to change the on-board jumper) and you can buy a break-out board as well.
The Starter kit provides many more peripherals.
I mainly use the Bemicro for NIOS II/SOPC development and for testing small chunks of Verilog/VHDL code. Compiling for the Bemicro is much faster than compiling for our actual boards (2 min vs 90min) because our actual boards require much more logic to be instantiated inside of the FPGA for minimum operation.
Other CIII kits (list from Digikey):
NIOS II CYCLONE III ED (EP3C25)
DEV DSP CYCLONE III (EP3C120)
EMB CYCLONE III EDITION (EP3C120)
DEV CYCLONE III EP3C120 (EP3C120)
DEV CYCLONE III LS (EP3CLS200)