1. with Nature's own hand painted: —In Shakespeare's time, the word for cosmetics was "paint"; here the poet is emphasizing the beautiful natural color of the young man, in contrast to the color of the paint that women use.

2. passion: 1) strong feeling, love; 2) expression of passion, love poem.

5. rolling: roving.

7. hue: color, form, appearance.  all hues in his controlling: i.e., being the epitome of beauty.

10. fell a-doting: 1) fell in love; 2) became foolish.

11. addition —What was added to the young man's form is strongly hinted at by the pun in line 13.  me of thee defeated: deprived me of you.

12. to my purpose nothing: i.e., of no use to me.

13. prick'd thee out: marked you out (with a sexual pun). —In the days before pencils, selections in a list would be recorded by pricking (making small holes in) the paper.