Matt had a good question: How do we type some of those obsolete kana like ゐ and ゑ? I found the answer in the Apple ことえり help file which, unlike most Apple help files, was surprisingly helpful. For the above characters you type WYI and WYE, respectively. Japanese is not the only language with this problem. I occasionally forget how I type nü using the pinyin input method for Chinese (the answer is a wonderfully intuitive nv).
UPDATE: In a comment to this posting, my mom added a great link to a page listing various special roman characters and how to input them. I guess I could also add a plug for my own Pinyin to Unicode Convertor website which you can use to create unicode pinyin with tone marks.
UPDATE: Adamu pointed out that this list doesn’t have the ヱ from Yebisu beer! The list below is all hiragana. If, while typing Japanese you type “wye” you get ゑ but if you type “wye” with the “shift” key down, you can get the desired ヱ that is familiar to beer fans in Japan.
Though this is not really related to the languages in your posting, I wanted to let you know about a handy site that I’ve used a LOT in the last few years (in fact, I keep a printout on my desk and frequently refer to it) namely http://www.typeart.com/special_characters.asp
(scroll down on the page)
mom
Ooops – ignore me and the above, I just noticed you already had a link to this site.
mom
You forgot ye as in Yebisu beer!