It's like asking where to visit in Canada, United States, or China -- the country is big enough the question itself is pointless. It depends on what kind of vacation you are looking for: natural scenary? popular scenary? shopping? urban centre (I am serious, some people just wanna visit those big cities, weird)? My personal favourite was the Osaka area with its less dense population (and friendlier people, IMO), Nara Park has lots of deers (which were extremely friendly), you can go over to Kobe and Shigoku area for their beautiful landscape (and of course, Sanuki udon!) Though I must admit, most people start with Tokyo.
I have been in Tokyo. If you are going to a foreign country where you have never been before. It is perhaps most common to visit the capital first and then gradually move to the more remote and exotic places. Need to warn you that Tokyo doesn't come cheap. Everything there needs lots of Yens But if you are in Tokyo, there are lots of things to do. If you like shopping you can go to Shin Juku or Ginza. If you like electronics, Akhabara. Or you can go to the many temples in this city to find some inner peace in this over crowded city. Very polite people, but please be warned, the Japanese don't speak English very well!!!
^ I went Tokyo before, and its nice just to see a new culture but be warned things are not cheap and not that spacious... The electronics over there are exactly the same price as it was in the UK, the only good thing is that things come out earlier there. But its worth going just to see all the sights and sounds. I also went skiing and to a hot spring up north but cant remember where...
Disneyland in Tokyo of course... I have been there when I was abt 8 years old... It was most fun & exciting place to visit ever in my opinion!