They have the standard QWERTY layout, with Japanese subtitles in smaller script below the English letter. Some punctuation keys are re-aligned for the digital world; specifically, those keys that are frequently used on the internet, such as @ and :, have been put in non-shifted position in order to allow faster typing of the sort usually done on the internet. (You have the option of leaving these punctuation keys how they are an adaptation we have come to love because it makes typing faster--or setting them to the layout you are currently accustomed to. The swap is done with one click of the mouse, and can be done at any time.)
What they don't tell you is that its impossible to "adjust" to this "new" layout, especially if you touch-type (Nobody in Japan touch-types, so this layout does not affect them. The keys are not simply "re-aligned" like they would have you thinking. They are in totally different places. In particular, important keys such as \, [, ], and _ are in absolutely wrong places. And this is not just a "keycaps" issue. Backspace is shrinked down to 1-key width, and there is a "backslash" key inserted between where "=" and BackSpace are in the U.S. layout. Note, that most of the extra "Jap" keys are NOT accessible when keyboard is not set in "Jap" mode - i.e. during boot, or while installing the OS, or if you don't load the "Japanese" keymap.
For an example of this, check out the illustration below, taken from (who else) www.dynamism.com:
Note oversized Enter key, "Windows" key right where it does not belong, lack of PgUp/PgDn/Home/End keys that don't require 2 keypresses to operate, right shift on the wrong side, and of course, the "aligned" punctuation marks above the numeric keys. The keyboard screenshot was taken from a Toshiba laptop, and I actually prefer Windows keys in the upper right corner of the keyboard as opposed to them wasting space next to spacebar/ctrl/alt keys etc.