My name is***** and I am sorry for the delay in answering you. I just logged on this morning.
First, how old are your kittens? How old is the momma cat? Has the momma cat had all of her vaccines? How is the remaining kitten doing this morning?
Based on your history, the first thing that comes to mind is a viral infection such as herpes or panleukopenia. These are very dangerous to very young kittens and can wipe out an entire litter. Older cats, when they become infected, are stronger and can fight off the virus, which is why your momma cat is still doing okay. If it gives you comfort, there was nothing you could have done differently to save the other kittens.
After the last kitten is weaned (or if she passes, :-( ) you will need to thoroughly disinfect your house with dilute bleach (1/2 cup in a gallon of water). This will kill any virus in your house and protect any future cats you bring in.
Also, once the kittens are weaned, it will be time to have your momma cat spayed so that she doesn't have any more kittens. She will try to get pregnant again as soon as she is no longer producing milk.
Does this help? Do you have any other questions?
Kansas State University,
College of Veterinary Medicine Class of 2001