Actually I recommend you keep the frame rate and aspect ratio the same as the original as some videos (especially if what you're encoding is a movie) maybe 16:9 and may use 24fps pr 25fps. It always safer to check what the original is and make sure its the same or else you can end up with elongated people or bad flicker and/or jerky movement. The video scale 640x480 is for 4:3 videos and 720x480 is for 16:9 videos.
I've used xvid and H.264 and haven't had a problem with the encodes ^^
#11 btw is for encoding from DVD files (VOB) as they contain a whole lot of extra information which you can use or discard like subtitles and other languages ^^