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Stanley at Wery Nice offers the following method for preparing ginkgo nuts for desserts:
You can use the canned version (in water), or those still in shell purchased in the supermarkets or the dried food stalls (干粮) stalls found in China Town, and in Singapore, Waterloo Street Market (四马路), Hong Lim or any branches of the Chinese medicine stalls in most shopping centers（like 福华 or 正中平）. You have to de-shell it by knocking it with something hard (eg stone pestle) to crack the shell, and then peel off the brown skin (boiling it lightly helps to remove it easily). If you use canned version, drain away the water.
Put the nuts in pot, and cover it with just enough water to cover all the nuts. Add in lots of raw sugar (or white sugar, but I prefer the raw sugar), about half the amount of the nuts in volume (approximately, the exact amount is not very crucial, as we just need it to be extremely sweet to allow the nut to absorb). Leave it to boil for 15-20 mins. Cover and leave it for at least 12 hours (prepare this the night before you need it the next day). Scoop out and drain off the sugar solution. Set aside to be added into your desserts like 清汤，腐竹糖水，莲子糖水。
Do not pour away the sugar solution; it can be re-used to sweeten the desserts that you will be cooking anyway.