Cyclone III and SDR SDRAM

3.3V SDR SDRAM can be operated with Cyclone III without problems, I just ported a respective Cyclone I design to Cyclone III. Regarding possible overshoots, the best solution is to prevent any overshoots by a suitable design. If the RAM is placed close to the FPGA, no particular means are most likely required. If external logic is driving 3.3V to the FPGA over longer distances than 2", it may need series termination (e.g. 50 ohms), if not yet included in the driver. This way, you are able to achieve a good signal quality with usual PCB wiring and don't need any PCI clamp diodes with on-board generated signals.