I think that if one of the supported display modes for the 1080p 96 is 720p, (which I do not know if it does yet for the 96), then they will look pretty much the same. If not though, I am unsure. That's just my guess, though.
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As an update, I was doing some searching on the Samsung website, and I came across the TV advisor which allows you to compare several TVs at once. When I went to compare the 46", Samsung gives a "minimal advertised price" of $4,799.99. For the 40", it's given as $3,799.99.