For long questions the "vertical" arrangement, no doubt. In the example, I'd indent the radios to make the document more scannable and to emphasize the dependency.
OT: But for short "questions" (actually, labels) I'd use a fourth arrangement, with the label like in the examples, and the options in a column (as in the third example) but shifted right so that the form has two columns, one for the labels and the second for the options.
This is the traditional 1-column vs. 2-column form layout. In the 2-column layout the "answers" don't get in the way for scanning the "questions" (labels).
Something like this:
Preferred color O green
Car brand O Ford
Notice the non-alignment of the options columns. This is so on purpose, because in lengthy forms a very regular pattern is not helpful for a user who took her sight from the screen to see a paper and has to find back her location.
Is like those forms where all inputs have the same size no matter the length of their content and returning to the current working location is difficult and error prone.