LVPECL with VCC of 3.3V on a Cyclone3

The quick answer: No.

The long answer:

The Cyclone 3 handbook says LVPECL requires VCCIO of 2.5 V, and is only available on Clock Inputs of Cyclone 3 devices (Table 6-4 on page 6-13 of the handbook)

That being said, quartus doesn't know what your real VCCIO is connected to, so you can say it's a 2.5V bank, but have it all hooked up to 3.3V, but the timing, and threshold levels wouldn't be guaranteed in this state, so it would be use at your own risk. However, if you state one item as 2.5V in the bank, (For the LVPECL), you would have to declare all IO's in that bank as 2.5V IO's, so you risk invalidating more than just the LVPECL thresholds and timing, but all the other IO's that are in that bank.

If you need LVPECL outputs, you need to have an external LVPECL driver anyway. Since the Cyclone 3 doesn't support LVPECL drivers.

Pete