Can 5V be applied to 3.3V "5V tolerant" ADC inputs for indefinite durations?
Yes, the ADC will read "max value" while the input is above the ADC reference voltage, and the internal ADC clamping diodes will be dealing with the over-voltage condition. The best thing you can do to ruggedize your ADC inputs is to use external schottky diode clamps to the 3.3V rail, and a series input resistor.







simulate this circuit &ndash; Schematic created using CircuitLab

Where R1 value is calculated to protect D1 and D2 from voltage clamp currents (based on the power rating of the package you choose) and R2 is optional, and is there for the same purpose - to protect the internal ADC input clamps from over-voltage currents. 

Ensure that the total input impedance from the input signal and through R1 + R2 remains within spec for the ADC input (check datasheets for this).