Nope, I don't think you're imagining things. I didn't realize it myself until this article appeared and I came across your comment.
I've done some web design, and so here's my basic <theory> below, typed as a stream of consciousness. As for making something look "Japanese", I think it's a result of various things:
Rounded Corners:
I don't these are strictly Japanese (see Slashdot's header, Southwest Airlines, Expedia, BBC (UK), Virgin Group (UK)). Though, rounded corners have made websites nicer to look at (not rigid - don't round/curvy things make people generally happy? Interpret as you wish.)
Pastel color scheme presence:
This may be a Japanese thing - all the non-Japanese sites I mentioned above generally employ primary colors. Two interesting US-based website examples are: Sprinkles Cupcakes and Pinkberry Frozen Yogurt. Both sites use lighter, non-primary colors and those color shades and combinations give me a sense of "fun" instead of "corporate". Note, though, that the different color shades aren't necessarily pastel-like in my opinion. One US-based website that uses something very close to pastel colors is Martha Stewart Omnimedia. We'll have to bring in a color expert to state whether Martha's colors are truly pastel.
At any rate, I think that only certain companies can satisfactorily use pastels in the US, and that would be companies dealing with fun food (cupcakes, frozen yogurt, etc) and hobbyist home decor arts/crafts. I think this is part to how I (and maybe you) without a Japanese background/surrounding/etc interpret colors and, as part of our respective cultures, have an understanding of what those colors represent. See this Visual Color Symbolism Chart by Culture and Color Symbolism Chart by Culture for a basic review. As noted in these two charts, "Green" in the US can mean money and trees and other things, but in China green hats mean a man's wife is cheating on him. One color, vastly different meanings! More information on "green" as a color: http://desktoppub.about.com/cs/colorselection/p/green.htm.
High-Context (Japanese) v. Low-Context (N. American, German-Speaking, etc) Cultures:
I came across this article while looking up cultureal color perception in Japan: Elizabeth Würtz's 2005 analysis titled: "A Cross-Cultural Analysis of Websites from High-Context Cultures and Low-Context Cultures". In this study, she noted that Japan is a high-context (HC) culture, whereas North America (and German-speaking countries even moreso) are low-context (LC) cultures:
Face-to-face communication in HC cultures is thus characterized by an extensive use of non-verbal strategies for conveying meanings. These strategies usually take the shape of behavioral language, such as gestures, body language, silence, proximity and symbolic behavior, while conversation in LC cultures tends to be less physically animated, with the meaning depending on content and the spoken word.
What was interesting to read were two of her conclusions regarding animation and presentation of individuals+products on websites:
Animation:
Tendency in HC Cultures: High use of animation, especially in connection with images of moving people.
Tendency in LC Cultures: Lower use of animation, mainly reserved for highlighting effects e.g., of text
Individuals separate or together with the product:
HC: Featured images depict products and merchandise in use by individuals.
LC: Images portray lifestyles of individuals, with or without a direct emphasis on the use of products or merchandise.
Example: Assuming you consider yourself as a member of a LC culture, would you trust the Home Depot or Lowe's to sell you a rotary saw if their website was in pastel or animated characters? Also, would you trust Intel to sell you an N-core processor if their packaging was in, say, hot pink?
"Chibi" characters:
Definitely Japanese. I have no idea why chibi characters make stuff sell so well in Japan. Maybe it's all the anime? Or Hello Kitty? Or, maybe it's so extreme in comparison to their formal culture and possibly corporate office culture, that anything diverting from the formality of all else is a winner (ergo, related to Japanese culture being a high-context one, as Würtz postulates)?
White space usage around text in general:
For example, from what I've seen this morning on random Japanese sites, the space between lines typed in Japanese tends to be far less than the line spacing you'd see on English websites. Compare the front pages of slashdot.org and slashdot.jp, specifically the spacing between links in the grey boxes on the right-hand sides. I think this is because almost all Japanese text characters typed out are the same height, whereas English text characters aren't typically the same height (ergo, English readers look for the line spacing). Also, notice that there are practically few hard spaces between words: "Hello, how are you?" in English has 4 spaces, whereas the same phrase in Japanese, written in Hiragana, has no spaces.
And, if you look at the kids' page on the NTT Japan website you linked to earlier, you'll see that the text on images have thick, colored outlines around each text character, as if to make the text character look thicker. From what I've seen, the few companies that I've seen do similar to their text characters are non-formal companies like Twitter, though even Twitter doesn't use that thick text character highlighting anywhere else on their site.
Of course, other languages may employ the same tactic of outlining most of their text characters, though those examples don't come to mind at the moment.
</theory>
There are probably other things that I'm missing. Any ideas, anyone?