In "My Last Duchess," the "blush" or "spot of joy" is the Duchess blushing. The Duke indicates that this blush is not because the Duchess is embarrassed or shy. Rather, he claims it is a flirtation. Therefore, the blushing "spot of joy" is a metaphor for flirtatious behavior.
Sir, 'twas not
Her husband's presence only, called that spot
Of joy into the Duchess' cheek; (13-15)
The painting itself is, "by design," the Duke's conception of his late wife. In the poem, he complains that she did not reserve her smiles just for him. He is jealous that she would give the same kindness to other men.
Oh sir, she smiled, no doubt,
Whene'er I passed her; but who passed without
Much the same smile? (44-46)
Earlier in the poem, the Duke says that he rarely reveals the painting for anyone. It is covered by a curtain. Now, the Duke can have the Duchess' smile all to himself. The painting, an object, is the way the Duke wanted the Duchess to be while she was alive: framed, still, obedient, giving smiles/affection only to him. Thus, the painting is a metaphor for the Duke's idea of ideal behavior for a Duchess. The painting is an object, a possession. The Duke objectified his wife in life and in death. The painting is not a memorial of his late wife; it is a metaphor for the Duke's insecure, jealous, and controlling behavior.
A metaphor is an implicit comparison or one that does not use explicit comparative terms such as "like" or "as". Normally a metaphor is described as comprising a "tenor" (the thing being compared) and a "vehicle" (what it is being compared to).
"Hands": One might be able to argue that "Fra Pandolf’s hands/ Worked busily" is a synecdoche (a type of metaphor in which a part stands for the whole) as the hands stand in for the entire artist, but one could also argue that it is not metaphorical, as one does literally use one's hands in the art of painting.
"for never read/ Strangers like you": This one is tricky. If he means "read" as we "read" text literally, then "reading" the painted image of a face or looking at it as though it possessed the same kind of meaning that language possesses could be considered a metaphor
"My gift of a nine-hundred-years-old name": The Duchess assuming the name and title of her husband is not literally the husband giving her a "gift" and thus we can say that the Duke is comparing the marriage to a gift he is giving a wife.