What type of stove is it?

I've flown with a small stove like this a few years ago: http://www.rei.com/product/660163

in my checked baggage and had no problem (no fuel cannister, obviously). Of course, it was probably fairly obvious to the baggage guy that I was going camping, considering that my bag was full of tents and sleeping bags and climbing gear. Now, of course, this isn't a guarantee you won't get a bag guy who's having a bad day and is feeling peevish. If you're really worried, you could just stop at an REI once you get to your destination and pick up a cheap model, the single-burners run for something like $30.

If you're feeling risky, and you have a stove with an external line you could probably rinse thoroughly with water and remove the residue.

Just buy fuel once you get to your destination.