To correctly render Hepburn Romaji in HTML, you must use the following entities. They use a macron, or line above the letter, to represent the long vowels.

Ā = Ā ā = ā
Ē = Ē ē = ē
Ī = Ī ī = ī
Ō = Ō ō = ō
Ū = Ū ū = ū
You can also use ̄ which is a combining character which will combine with any previous letter:
ā ē ī ō ū

When the macron is unavailable, the circumflex accent is usually used: â ê î ô û
Sometimes the diaeresis (also wrongly known as an umlaut) is also used: ä ë ï ö ü
Jeeves has chosen to use a tilde in his writeups, which is probably equally acceptable though I haven't seen it used this way in print.