When you work with a language like Japanese where the writing system is different from the Latin alphabet, transcription is mandatory. There are several transcription systems for Japanese and anyone learning the language ought to know about them.
But first of all, when do you need transcription? When you translate or adapt from a Japanese source. There are always several possible translations and thus several possible transcriptions: you have to take into account the audience, the context and the aim of that transcription.
Let's have a quick overview of the main systems.
The Hepburn system is by far the most well-known and used internationally. It's said to be close to the Japanese phonetics but I don't fully agree on that. Anyway, it's the most practical one when dealing with people who don't speak Japanese. The consonants are based on the English language but the vowels are closer to Italian so you may have to explain the pronounciation.
The second main one is the Kunrei system (Kunrei-shiki). If Hepburn is phonetical, then Kunrei is phonological, i.e. it's the mental representation of the sounds of Japanese. And so the audience needs to know Japanese. That's why it isn't used much outside Japan and not very well liked by the non-Japanese. Which is unfair. It's actually very practical when studying or teaching linguistic phenomenons. Like for example the verbal forms. If you say the conjugation of yomu is yom- followed by different vowels yom-a, yom-i, yom-e, yom-o, then you have a problem for hanasu since it gives hanas-a, hanas-i, hanas-e, hanas-o. If you use Hepburn hanashi needs further explanation. The same goes for rendaku (sequential voicing) : yo+sakura = yozakura, hosi+sirusi = hosizirusi whereas with Hepburn you get hoshi+shirushi = hoshijirushi.
Here's a summary of the above transcriptions, when they're different Hepburn's in red and Kunrei in blue.
a i u e o ; ka ki ku ke ko kya kyu kyo ; ga gi gu ge go gya gyu gyo ; sa shi/si su se so sha/sya shu/syusho/syo ; za ji/zi zu ze zo ja/zya ju/zyu jo/zyo ; ta chi/ti tsu/tu te to cha/tya chu/tyu cho/tyo ; daji/di,zi zu/du,zu de do ja/dya,zya ju/dyu,zyu jo/dyo,zyo ; na ni nu ne no ; ha hi fu/hu he ho hya hyu hyo ; ba bi bu be bo bya byu byo ; pa pi pu pe po pya pyu pyo ; ma mi mu me mo ; ya yu yo ; ra ri ru re ro rya ryu ryo ; wa o ; n.
There's a third system, the Nippon-shiki (or Nihon-shiki) but it's pretty much similar to the Kunrei so I'm not talking about it here.
You may have already noticed but I use Hepburn for this blog.
In the above systems, long vowels are written with a macron but sometimes a circumflex accent is used (because it's easier to type). So, no, おう is not transcribed "ou". But sometimes for names such as Yû or Kô since they're so short they can be written Yuu or Koo or Koh. And here we have the appearance of the h. It comes from the typewriters: if you type two letters that are close to each other the typewriter gets blocked (hence the azerty, qwerty, qwertz keyboards). So for a surname like Ôtani writing Ootani wasn't possible so it became Ohtani. Or sometimes long vowels are just discarded.
For the えい pronounced in standard Japanese (i.e. Tokyo Japanese) like a long e, you can find "ê" instead of "ei".
For the n before a vowel it's supposed to be followed by an apostrophe but you can also find a point. 谷崎潤一郎 gives Tanizaki Jun'ichirô or Tanizaki Jun.ichirô. Before a labial (m,p,b) since it's pronounced m, some people write it m for example Asashi shimbun. Offically it's still n though.
Lastly, the gairaigo. In all academic works (like a thesis) you're supposed to transcribe everything as if it was of Japanese origin: コンピューターis konpyûtâ (or kompyûtâ). Some people prefer writing the loan words with their original spelling. That's usually what I do too unless the word is a very old loan word and feels Japanese to the Natives, such as kappa and pan (from the Portuguese capa and pão), kokku (from the Dutch kok) or zubon (from the French jupon). There is also the matter of the wasei-eigo and ryakugo like gasorin sutando (gasoline + stand) or rimokon (remote+control). I'd say this is left to your own discretion, for my part I use the English spelling for the first and the Japanese pronounciation for the second.
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