Being a tourist myself, there is no way that I can properly comment on the changes in these years. I think people like NyGuy, ... etc can tell us all the interesting differences then and now. What I am trying is to provide similar perspectives. As built a city as NYC, it's amazing that you can still see the significant change of the city.
All pictures are mine:
June 2003:
January 2009:
So bad that I can't find a 2003 picture of mine that has the Jersey city side:
2003:
2009:
Downtown is healing itself:
2003:
2009:
More to come if you are interested.