"Mostly" is the only one out of the three that can refer to non-temporal situations. "Often" and "most of the time" both always refer to time. ("I eat chicken often. It tastes good most of the time. Chicken is mostly made of protein.") "Most of the time" suggests a slight emphasis on its exception-- it is often followed by a description of what happens the rest of the time. ("Most of the time I eat healthily, but sometimes I eat an entire gallon of ice cream.") Hope that helps!

'Most of the time' is closer to 'usually' in meaning. You would expect this to be around 70% or more. 'Often' is more in the region of 40 - 70%. 'Mostly' is also around 70% +, but it doesn't often refer to time or frequency. You use it for other situations, such as 'Our clients are mostly from Japan'.