Short answer:
This depends on your needs. If you need to store temporary results with maximum quality for further editing, I recommend using a lossless
codec such as Lagarith or Huffyuv. They will keep every bit of information.
If you need a high quality codec to save final results into file which will be only played but not edited, then MPEG4 implementations like DivX and XviD are a good choice.
Long answer:
read here.