Cyclone III devices are much more powerful compared to Spartan 3 series at the same cost.
I am not sure if that is true for Stratix III vs Virtex-5. Choose from either Altera or Xilinx, as they are fierce players in the FPGA market and are here to stay. Both of them have excellent tools and tons of documentation and reference materials.
Also Stratix devices have a defined path to structured ASIC via Hardcopy series. Xilinx has EasyPath series, though it is still an FPGA solution.
Xilinx is for some reason relatively popular compared to Altera, IMO.