Should be able to get higher quality doing a manual rip than AutoGK, not lower quality. That is I guess if you have some idea of what you are doing.
ARCalculator is also worth checking out. For XviD it is able to run an additional pass and use the XviD stats file for conditional filtering based on motion. So low motion sharp resize, high motion blured resize, etc.
If you have a network it is also worth checking out the AVISynth TCP preview plugin. With it you can have one PC do all the decoding/filtering and the other the encoding.