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Frame-based means Progressive, which means the entire picture will be displayed in a single pass. You would use this if you were authoring a video at 23.976 fps (NTSC), 25 (PAL), or 24/30p BluRay, or if you were encoding for playback on your PC only. You would only do this is your source was also progressive or you had some pretty good deinterlacer in play.
Lower Filed First and Upper Field First (also knows as Bottom Field First and Top Field First) relates to interlaced encoding. Most CRT televisions display the image in two passes (or Fields), showing each alternate line in each pass. They do this fast enough that persistence of vision allows us to see a single image (although the eye is good enough to discern some flicker, which the brain usually filters out). BFF/TFF (or Lower and Upper, in your case) refers to which filed gets displayed first. Mini-DV, for example, is always BFF. Mpeg-2 can be TFF or BFF, but is usually TFF.
If you mix up the field order you get jumpy playback of action and movement.
Which gives higher quality ?
None of them. It depends on the situation. If you have interlaced source and intend to view the image on a standard TV (or even a new TV) then you are better off encoding interlaced and letting the TV take care of the display. Poor conversion from interlaced to progressive can be horrible to watch.Read my blog here.
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I recommend you maintain the field type of your source video. If you do not know what it is, download the free program GSpot (in the Tools section of this site). Open your source video in GSpot to determine the field order and frame rate. Also, keep the video standard (PAL, NTSC, or SECAM) of the source.
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I changed the subject so it better describes your topic.
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