For smoothscale/rotozoom, in terms of pixel art, preserving the pallet is often a priority. Smoothscale and rotozoom do not, I believe preserve the pallet. They add colors as needed to make the gradients smooth and such.
As for standard scale and rotate, they do not do this. I also make the assumption that they should be faster than smoothscale and rotozoom but haven't tested the theory extensively.
I should also mention that it is also very common (because scaling and rotating is so useless on pixel art) to make prerendered rotation frames. Drawing these is tedious as hell but it at least guarantees all the frames look nice.
Lastly, it might be obvious, but I should at least mention that you should always scale and rotate your original image. These processes are destructive and when applied cumulatively you will eventually be left with a mush.
Edit: Oh and rotozoom only lets you scale the width and height by the same factor. The two separate scale functions let you scale width and height separately.