A great website discussing the meaning of nursery rhymes:
Three Blind Mice rhyme

The origin of the 'tale' of Three blind mice!
The origin of the words to the Three blind mice rhyme are based in English history. The 'farmer's wife' refers to the daughter of King Henry VIII, Queen Mary I. Mary was a staunch Catholic and her violent persecution of Protestants led to the nickname of 'Bloody Mary'. The reference to 'farmer's wife' in Three blind mice refers to the massive estates which she, and her husband King Philip of Spain, possessed. The 'three blind mice' were three noblemen who adhered to the Protestant faith who were convicted of plotting against the Queen - she did not have them dismembered and blinded as inferred in Three blind mice - but she did have them burnt at the stake!