As far as I know only three words (or particles) have irregular, non-phonetic spelling in Japanese:
- "は" - The topic particle is pronounced "wa" but the kana is otherwise pronounced "ha"
- "へ" - The movement towards particle is pronounced "e" but the kana is otherwise pronounced "h"
- "を" - The kana is only used for the object particle as far as I know and in the kana table takes the position of "wo" but pronunciation seems to hover somewhere between "o" and "wo"
So did the sounds of these particles change since the spelling was set down? Or were the spellings intentionally chosen for some reason? Are there any other irregular kana spellings I omitted?
(P.S. I found the question Why is は pronounced as わ when used as a topic particle? while working on this question but since mine is broader I decided to go ahead anyway, plus it might give an opportunity to test our duplicate marking strategies here)
Some of the comments to Lukman's answer below suggests that these might not seem like irregular sounds or kana to native speakers. I was surprised that people interpreted this question to be about romaji rather than being about kana and particles as I intended it.
So a further question: Are these particles and their kana and pronunciations seen as irregular by native Japanese speakers? Or just to learners of Japanese? And what do Japanese and non-Japanese linguists think?