Why don't you check the official statistics?

Issued Visa in 2008 by Mofa@Japan

Total 1,512,018
1 China 759,694
2 Thai 171,503
3 Malay 92,612
4 Philipin 75,508
5 Indonasia 59,175
6 Russia 57,964
7 India 46,782
8 Brasil 31,819
9 VietNum 23,944
10 Korea 23,110
11 USA 20,739
12 Mongol 7,824
13 SriLanka 7,579
14 Nepal 6,417
15 Taiwan 5,573
16 UK 5,549
17 Pakstan 5,526
18 France 4,441
19 SouthAfrika 4,373
20 Germany 4,240
21 Myanmar 4,227
22 Uklina 4,150
23 Vangradish 3,963
24 Iran 3,720
25 Peru 3,504
26 Canada 3,220
27 Egypt 3,200
28 Rumania 3,196
29 Australia 3,190
30 Colombia 2,929

In 2007, total 1,396,008 and in 2006, total 1,187,218.

You can refer to the original data at http://www.mofa.go.jp/mofaj/toko/tokei/hakkyu/
(In Japanese).

So around 1% of the population...

That isn`t quite right as it`s only the number of visas issued during that year.
More accurate data would be here;
http://www.moj.go.jp/PRESS/080601-1.pdf
Unfortunately I can`t find the same document in html, but here is the same thing from 2006; http://www.moj.go.jp/PRESS/060530-1/060530-1.html

It has a nice breakdown of the number of foreigners and their countries of origin.

But still far from the "over-crowding" the OP describes in the first post.

Interesting to find Colombia listed in the top 30.

so it's still 1% or more? and couldn't read what was there in that pdf file since it was filled with dots everywhere..

Saw more gaijin then I expected in Tokyo but still it was only a handful.

As for it being crowed I think your thinking of China.

Only lines I saw were for certain things like restaurants or events and even those were few and far between.

I find Manhattan WAY more busy and the subways more crowded.

Even if you go to places when you expect to see gaijin (like a Irish Pub, MMM probably knows the Blarney Stone), there are still more Japanese there looking to meet gaijin. Most gaijin I saw or met were tourists that didn't live there.
Japan is a crowded country in the cities, but mostly with Japanese. The countryside is nice and open.

Yes, I know the Blarney Stone...most of those gaijin bars seemed to be filled with gaijin students, tourists, and new-arrivals, as well as Japanese who like the atmosphere, hearing English and cheap drink specials.

Thank you for your pointing out. I could not find the amount who are in Japan legally without visa.

The difference between yours and mine are the 一般永住者 and 特別永住者.
Do you know what the 特別永住者 is?

I see. 特別永住者 are the foreign people and their descendant who was in Japan as of Sep/2/1945.