depends on what you are trying to do. Milkshape3D can be great for somethings, and others...well, not so great.
When I do use MS3D, I maximize the one pane, position the object using the numeric keyboard inputs, and then take a screen shot. I then move over to photoshop and cut the image out (with no anti-aliasing), and then shrink it down to the predetermined height. From there, I just repeat the other steps and plonk them in the same file on a black background (so that you can have transparency).
Make sure you don't use antialiasing in your selection tools or you'll get fuzzies (the opposite of jaggies) on all your sprites.
-= i only do what my rice krispies tell me to do =-