I'm assuming you're talking about a liquid-fuel (white gas) stove.

Consider rinsing out the bottle repeatedly with water, filling it with water prior to the trip, and packing it as carry on. If someone bugs you about it, be prepared to drink from it (seriously) and show them there is no fuel smell. If you put it in checked bags you risk some screener pulling it out and trashing it because they think "fuel bottle" is a dangerous device.

I've always thought it would be a good airline/screener common sense test to check a (never used) 5-gallon gas can as baggage. My gut feeling is that many agents/screeners would freak even though it is really just a plastic container no different from luggage.