communication with 3.3V devices with cyclone 3

Regarding voltage margin, 3.0 V may be a compromise. Also most 3.3V logic devices could operate at this supply level. Series termination of fast outputs should be considered with trace lengths above a few inches to my opinion. Devices as AD converters have typical 50 ohms series termination, most programmable devices have the option anyway. You may determine the necessity for termination from measurements, a low capacity active probe and an above 500 MHz oscilloscope are required however for a realistic display.