Legs are tricky. I've found that it usually turns out straight when I measure both from the top down and bottom up. If they are different from each other then I usually follow the bottom up measurements. Also, make sure when you're measuring and cutting that the pants are folded right. Don't cut with the pants opened up. Fold the pants in half with the inseam NOT on a fold, but in the middle (like when ironing a pair of slacks).
There's more info on altering pants in our blog. Check out this article for more altering ideas:
http://sewmamasew.com/blog2/?p=487Hope this helps!