For
the most part, puppies cry at night because they are lonely and afraid.
It's a lot to expect of a puppy to quickly adapt to a loss of familiar
surroundings, siblings and mother. Left alone at night, in a crate,
far from contact with its adopters doesn't help either.
You should keep in mind that your puppy is learning 24 hours a day. If the puppy cries and your reaction is to open the door crate, he’ll keep doing what works for him and you’ll never get any sleep.
I would recommend that you start to use the crate more during the day time. Feed your puppy its regular meals in the crate. When a treat is in order, give it to him or her in the crate. Puppies sleep a lot during the day, so use the crate for nap times. Use a crate that you can move about the house with you. Decide which chew toy your puppy most enjoys and provide it exclusively in the crate. Keep associating the crate as a safe and secure environment. Then the crate can bring comfort during those times when there is no choice but to leave the dog alone. During your puppy's early months, it is best to keep the crate right beside your bed. In time, you can gradually move it to wherever might be more convenient.
Breeders could make their puppy's lives a lot easier, not to mention their adopters if they placed a crate in with the litter right from the beginning. Eating meals and sleeping in a crate would provide a sense of safety and security in a crate environment. Instead, the puppy is popped into a crate, taken away from his mother and then left in one overnight, far from their new guardians. You can understand how they might have negative feelings towards something that is supposed to be a positive experience.
I'm not particularly convinced that the "give the puppy an item of your clothing or a towel with its mother and littermates' scent to comfort it" makes much difference. Same goes with the ticking clock, etc. On the other hand, I can't see how it would do much harm either, unless the puppy takes out its frustration on the item and chews it up, thereby, learning to chew fabric when it's anxious. Some people recommend a warm hot water bottle, but once it cools down it will leach the dog's body heat and make it very uncomfortable, so I wouldn't recommend it.
Understanding and patience for the first few days is in order. The crying will subside once the pup gets used to its new environment. If this has been going on for a while and you've been responding by letting the pup out, it will take longer, and for the short term will likely get worse as the puppy will be used to getting a response from you.
Animal Behaviourist John Wade (http://www.johnwade.ca/)