My research says Japan has several prefixes, 0120, 0800, 0088, 0531, although not all phone numbers in these prefixes are available to all callers.
In the US, holders of a toll free number pay their carrier a per minute rate (sometimes with billing increments of 1 second), as well as a fee per call from payphones.
The per minute pricing is pretty reasonable typically one or two cents per minute; I think the per call cost from a payphone are more significant, although I don't see this listed by most providers; I seem to recall it being pretty hefty (and some toll free numbers would not accept calls from payphones as a result), but maybe changes in the network and intercarrier billing have resulted in a smaller fee or it's just not relevant to most people because payphones are hard to find.