I tend to think they mean what the speaker wants them to mean. The difference isn't really well defined. To me, 'fairly' is the stronger of the three, and 'rather' is the weaker of the three. In other words, 'fairly good' is usually better than 'rather good'.

In some sentences, these three words mean similar things. For example, if you say, "It was a SOMEWHAT tall building", you could also describe the building as "rather", "fairly" or "pretty" tall. The word "pretty", however, is considered informal in most dictionaries and should be avoided in serious or business conversations.

Please state the context to enable this question to be answered.