Weather Conditions
The weather is one of the biggest deciding factors when determining how long to leave stain to dry before applying a second coat. The stain will dry much quicker on a warm, sunny day than on an overcast and windy day. Similarly, the more humid it is, the less time the deck will need to dry.
Manufacturer's Instructions
Unfortunately, there's no universal time limit on drying stain so the length of time the process takes also varies by product. Most manufacturers include instructions, often on the box for the product. They will likely give you at least some indication as to how long to wait before applying coat number two.
Bottom Line
In most cases, 48 hours will be plenty of time. BrightonServices.com suggests 24 to 48 hours, depending on conditions, so waiting two days will allow the stain to dry completely. In good conditions, one day may be enough but if you have any doubt, ExtremeHowTo.com suggests that taking your time is key to staining your deck.