Q: Is there a way to tell the difference between male and female gingko seedlings, before they're big enough to start producing that stinky fruit?
Unfortunately, there's no tried and true method for determining a female from a male ginkgo until it reaches flowering and fruiting age, which is usually around 20 years.
Nurseries propagate ginkgos by grafting a known male onto a seedling rootstock, thus you're pretty assured of a
male if you purchase from a reputable source.
If you grow a ginkgo from a seed, you take the chance of finding out about 20 years later that you may have a female. If you plant it far enough from frequently-visited areas, the smelly fruit may not be a problem (unless you're downwind of it!).
I recommend purchasing a known male sapling from a nursery or garden center. You'll be much happier (and your olfactory glands will be, too).