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After choosing System Config. Choices are:
System Configuration (referring to the PS2 itself) - Lets you see your PS2's information. Available information is console model number, MAC address, DVD Driver version, and PlayStation Driver version. It also has another choice that you can change. I think it's the Diagnostic option. It can be toggled to '"shinai" or "suru" which I believe is Off and On, respectively.
Date and Time - This lets you set the PS2's clock and adjust several settings on how the time and date is displayed. You can also pick your location and time zone.
Screen Display - This lets you pick the screen ratio and component output signals.
Sound - This has something to do with sound output, probably the optical output.
Display Language - This lets you choose the language that PSBBN displays in. The only current choice is Japanese. Maybe they plan to release versions with other languages in Japan eventually or they're planning for an eventual foreign release, like in Europe, where several languages would be neccessary.
Input Method - This seems to adjust how keyboard input works. There are two menus. The first one has settings to Romaji Input and Kana Input. The second has choices of Config 1 and Config 2. The first choice affects whether you have to enter romaji to type kana or just plain enter kana (only easy if your keyboard is labeled with kana on the keys). My keyboard has both Roman letters and kana on the keys.
Keyboard - This lets you specify what type of keyboard you are using, if you are using one. 3 menus appear. The first offers choices of Japanese Keyboard and English Keyboard. The other 2 menus I can't read or the choices for those menus.
Mouse - Lets you specify information about your mouse, if you are using one. The first option has choices for left-handed and right-handed mouse. The next two are for Mouse Scroll (something) and Double Click (something). I can't read the choices for either one.
UPDATE for owners of model 50000 or higher
There is an additional option at the bottom of the System menu. It's for the Remote Control. All it seems to do is turn the IR port on the front of the system on or off, so you can tell it whether or not to respond to the use of a PS2 Remote Control.