You can use the dark green parts for stocks, just freeze them until needed. But yes, like PP, just use the last 3 inches, where the white part and light green part is. Dont forget to remove the roots and clean out!
It depends on what I'm making. If they are going in a soup, I'll cut a v shape, cutting off the dark green parts of the leek that go out, and leaving a long peice of usable leek. if it's going in something else (sauted leeks or something) then I'll just use the white and light green.