When i want better quality i use double pass encoding ad 512/128 or 640/128-192.
Lower frame rates->higher quality, however, reducing the frame rate may affect the smoothness of the playback.
But, if you change frame rate, you can have video and audio out of sync.
If you have sync problems, my suggestion is to not change frame rate (leave the box unchecked) and use mplayer instead of built in media player.
Two pass encoding give you a more efficient encode when comparing to one pass but it usually takes at least double the time as the one pass.