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Love/hate Planet-X, but the double wheel bag from them is excellent value. I paid £15 each, since prices fluctuate it's a little dearer now. It helped me when I took my bike on the plane, surprisingly good quality. Since the price was less than most single bags elsewhere, I bought two and considered one side as extra padding/storage.
http://www.planetx.co.uk/i/q/BAPXPDWB/planet-x-padded-double-wheel-bag
They fold fairly okay, too.
Unless it's a really fancy bike I'd just use some bubble wrap / cling film / brown tape etc and pack them in there, wouldn't bother with a wheel bag.