There really isn't any difference in the three expressions. "Come into effect", I have rarely used this expression in my lifetime. "Go into effect" and "take effect", I have used often. Both mean the same thing and are understood the same way, but using "go" softens the statement a little.

They can be used for different subjects. A law, for example, would come into effect. I suspect that the difference between 'come into effect' and 'go into effect' may be a regional one - the previous answerers, all Americans, rejected 'come into effect'. However, for me, 'come into effect' sounds more natural than 'go into effect'. Meanwhile medication would only 'take effect'. Basically, 'come/go into effect' means to be implemented, while 'take effect' means actually have an effect. This is why all the phrases could be used for legislation, but only 'take effect' could be used for medication, drugs and so on. I suggest you google some examples to get a feel for the slightly different meanings of these phrases.

The above answers are all correct and insightful. But I'd like to add that there's a bit of a difference between 'take effect' and 'go into effect.' The latter typically refers to something that will happen in the future. For example; 'These changes will go into effect on May 17th.' However, 'take effect' can also be used here. But there are certain instances where 'take effect' sounds more natural. For example, if you're taking a sleeping pill tonight but it hasn't started working yet, you would say it hasn't taken effect yet. 'Go into effect' seems to be used more to refer to new sets of rules or standards or changes to something. I don't think I've ever heard or used 'come into effect.'

Jeff is correct. Su.Ki makes several good observations, as usual. I'm not sure that 'come into effect' is necessarily a regional American usage. I don't recall ever hearing it used nor having used it in my 54 native-born years here in the USA. It sounds very British to my ear. But maybe someone else has heard it here. I'd be interested to hear from that person.

There's no difference. They are all the same idioms.