I've only used B3 and Laver & Wood so far.
B3 is absolutely fantastic. I've gotten multiple bats from them, and its always such a pleasure dealing with them. As others have mentioned, service after getting the bat is tremendous. If they make a mistake they will rectify it without a second's hesitation. If your email doesn't get answered, I would just call them to follow up. Streaky is one of the nicest guys in the market and getting a Skype consultation is so much fun.
L&W: Very responsive to initial questions etc. Slight frustration is that its hard to actually talk to James himself but Anthony is super helpful. Once you put down your deposit / payment, James is a lot more accessible and you can discuss specifics to the Nth degree with him. And he is very knowledgable. Email response varies, but again, you can always follow up with a call if you think your email is lost. Worth mentioning that I was initially put off by their bats, because I thought they only make certain pre-set shapes, but that is not true. Its a fully customized service - you can specify whatever you want.
Both these two let you choose your cleft (as does every other custom bat maker now, if I'm not mistaken).
ONE BIG PIECE OF ADVICE: be VERY VERY specific with everything, no matter who the custom bat maker is. If you're picky about things, DO NOT ASSUME ANYTHING. You HAVE TO SPECIFY everything, even if you feel silly doing it. I feel that if you do that, you will avoid some of the problems mentioned earlier (getting a tiny bat that is made from a super dense cleft, wrong grade, wrong weight, etc etc).