As I type this answer, I am at a public library on an Indian reservation in New Mexico, so one of the legacies of Manifest Destiny is readily apparent, and I suppose if you asked any Native American, the answer would be something along the lines of cultural and linguistic genocide, not to mention physical genocide and subjugation. Of course, we would not be an empire without the completion of Manifest Destiny, and our prosperity and wealth are directly related to the taking of 3 million square miles of resource rich farmland, and the removal of those who already lived there.
I think that Manifest Destiny has transformed into being more about policies than territories. We are not so concerned with occupying other countries, but we do want them to have the same or at least similar policies that we have in the US.
It may be worth paying attention to the concept of "Manifest Destiny" as battles over the Arctic Passage heat up. The north, which has long been considered Canadian territory -- at least, according to every map and globe I've seen since I was a child -- is becoming a contentious area, with America, Greenland, and Russia all staking claims to this emerging trade route. Will America invoke God's blessing while trying to gain control of this territory?
I would suggest that we don't necessarily feel comfortable openly taking territory from other countries but we aren't shy about trying to get what we want and using whatever means necessary to get it. So even if we aren't taking over Iraq, we are willing to go to great lengths to get favorable deals on their oil and get American companies in there to profit from its development.
This is a massive topic and you will receive a real diversity of different opinions! Personally, I think that the whole concept of Manifest Destiny has decreased since George Bush Junior left power and Obama took office, although it is still very much alive and kicking. Manifest Destiny concerns the way in which America, by divine right or choice, was made a superpower in the world and therefore was free to interfere in the politics of other countries as it liked. Although Clinton's disastrous Somalia invasion...
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showed the limitations of this view, arguably Bush's foreign policy represented a new stage of this approach. However, fortunately, Obama seems to be steering America on a less problematic course.
You could argue that the idea of Manifest Destiny remains with us today because we continue to try to remake the world in our image.
One aspect of Manifest Destiny was the idea that we had the best culture and government in the world. This gave us the right to spread out and take more territory so as to put more of the world under that culture and that government.
Today, we no longer believe that we have the right to more territory. But we do believe that we have the best system of government. We have gone to great lengths to try to make other countries of the world be more like us (Iraq and Afghanistan come to mind). This can be seen as evidence that the idea of Manifest Destiny remains with us today.