Can I turn PCI clamp diode on in Stratix®, Stratix GX, Stratix II, Stratix II GX, Arria® GX and Cyclone® II devices with external series resistor to make them 5V compatible?

Yes, the input path is protected by PCI Clamp diode when you turn them on. Optional PCI clamp diodes are only available in column IO pins. Protection is achieved by clamping the pin voltage to VCCIO 0.7V which is within the absolute maximum Vi. The VCCIO will be forced to 3.3V when PCI clamp diode is enabled. The solution given in Cyclone handbook which explains the implementation of PCI clamp diode with external resistor can be applied to all the other devices which are not 5.0V tolerant. The link to Cyclone handbook chapter 11 is stated below:

Using Cyclone Devices in Multiple Voltage systems (PDF)