MeGUI gets another vote. The interface makes it a lot easier to customize/tweak encode settings all you desire. The hard part is figuring out what encoder settings strike the best balance between encoding speed and final picture quality. Sometimes, you can more than double your encode time (which is a lot when you are comparing 12 hours to 24 hours!) with no perceptible gain in picture quality. An x264 encode (opensource encoder) targeting a video bitrate of ~1.5Mbps for DVD-resolution video works fine and should please most people.
Try loading the DXVA-SD-HQ profile, drop 'Number of Reference Frames' down to 4 from the default 8 and give it a whack. You should be impressed with the results. Run a test encode with another profile like DXVA-SD-Balanced, same target bitrate. Determine if the tradeoff in speed/quality is worth it.
Edit: I posted a link but the Wiki linked above has a better page explaining all the options. Definitely give that a read, I'm doing it too!