Japanese input in romaji is the "mainstream" method in Japanese word processing. Although the hiragana input method is faster, most people do not learn how to do it, because the keyboard use is entirely different from the alphanumerical layout. I've only seen data input professionals use it but not among "regular folks," Japanese or otherwise.
Japanese language input is the same for both Japanese and non-Japanese Windows, so long as the Japanese language pack is installed. (Necessary for XP but included in Vista.) Keyboard setup may be different, but adjustments can be made on the Language option in your Control Panel. In short, no need to get Japanese OS or keyboard.
Issues related to Japanese language input are discussed here:
How to Type Japanese
If you're talking about adding small hiragana characters over kanji (adding "rubi") for greater ease in Japanese kanji reading for the reader, it is not the function of Japanese IME. AFAIK, you need word processing software such as Microsoft Office (Word).
The thread has been moved to "Learning Japanese."
Added:
Rubi tags appear to be possible in html, which is visible on IE but not other browsers. The discussion is here:
Ruby function discussed at Teach Yourself Japanese