I've tried everything from separating the papa mouse away from the colony, to having colonies that are together practically from birth. After two years I'm still experimenting with what works best, but what I know works best so far:
Usually I start with a group of 1.3 to 1.5, occasionally, for my six larger cages I start with 1.10 to 1.12 knowing I'll have some attrition, or that I'll end up separating out momma mice from that group to take to the petstore They pay $0.45 store credit even for pinkies, so sometimes when I have an overload of mice, I just take in five or six nursing momma mice with 18 or so babies each, and wham, I pay for the next couple months mouse food and bedding.
I've found that leaving the male in with the females is absolutely the best way to go about it. If the male dies I wait until the babies are all grown, and if I want to continue the colony, I usually leave a male baby to grow up with the females. MOre often I just feed them off. Right now in the winter with most of my snakes sleeping I tend to take them to the petstore more than anything else.
In my largeest colonies, in the big cages the colonies tend to metamorphose, the original females eventually get worn out and some of the female babies are left in the cage to grow up and replace their mommmas. In the groups that have this ongoing lineage of female babies replacing older females, and later a male baby replacing the papa, are my best long term colonies. Eventually the age level of the mice in the colony is varied, and about one female will pass on every six to eight weeks, in a group of 12 females and one male, it's a nice working solution. These are my fancy mice though, that I'm breeding for fancy characteristics. I tend to have the patience to wait for them to grow up a new male or females as needed and don't mind if they have a month or two without any offspring. The cutest babies go towards further breeding or are sold as pets, the rest go to the snakes, just like the albinos and the black and the brown mice.
As far as cannabalism, I've never really come to pinpoint this with any accuracy... often new mommas, if they don't have an older established momma mouse, will eat their babies. But I also get cannabalism in other certain situations... sometimes it gets too darn hot, and the mice kill more babies than they let live. Another issue I've found that often leads to losing babies that are older than a couple of days is if one of the momma mice is having difficulties in labor... I've had several mice that have ruptured their uterus and were unable to give birth, no matter how hard they struggled to give birth... every contraction would just push the babies into the abdominal cavity... and often in their pain and perhaps instinct (?) they would start massacring fuzzies and even hoppers. I've done a few C-sections on these mice in curiousity, and found it to be a ruptured uterus in all but two cases. In one case it was a herniated uterus, with a dark black mass all twisted up, and in the other case the mouse wasn't even pregnant, but instead had a tumour about the same size as the litter of 20 pinkies I was expecting. When mice are sick, they kill baby mice. Don't ask me why.
To keep my mice the most content, I clean their cages twice a week (Sunday and Wednesday), change their water at that time. I give them 3 to 4 days food with each cage cleaning. Their bedding is 1/2 pine, 1/2 alfalfa hay, with a bit of raw cotton in the winter for them to make warm nests. I feed them "Adult" dog food from Petsmart... dunno what else it's called, but it's their cheapest dog food and the mice love it and cannabalism rises every time I try to switch to another dog food. Along with the dog food they get COB which is a feed mixture of Corn Oats and Barley. I buy the dogfood and feed in 50 pound bags.... a 100 pound mixture of that lasts me about 6 weeks (6 large cages of mice, 25 small cages, 2 ten gallon aquariums, and one large hamster cage all of mice, plus 3 cages of rats, and two cages of gerbils) A bale of hay and ten bags of pine last me about 4 months. The cotton I pick up off the side of the road since Cotton is the major agricultural industry in this rural area. I don't disturb the mice too much during the days I'm not cleaning their cages, except to check on specific mice that have some special need. They produce like crazy. I was doing the math on how much the mice brought me in (not to mention feeding my 50 snakes) and reckon that they brought in about $750 in just selling my surplus to the petstore. Of course they cost about $225 in bedding, and $90 in food over the course of a year also.
Anyway, anybody who read this far probably deserves a medal. I'm done rambling. 
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~Sasheena
