Wapuro Romanization

This is the least confusing system to follow, in my opinion, if you are learning Japanese or want to keep things simple. It is very literate, and follows the logic of using the same romanized letters as seen in most kana-romaji charts.

While Kunrei-shiki and Nihon-shiki follow closely to the kana, and are common in native speakers, it's not the best way for foreigners to learn, since the spellings such as "si" "tu" and "ti" are pronounced dramatically differently in Japanese, and may cause confusion, to non-native speakers.

Typing in Modified Hepburn or Wapuro's variant form can cause misspellings, misinterpretations, and errors when using most IME and word processors, and many people are unable to freely type the macrons used in Revised Hepburn with a standard US keyboard, causing many to simply type a single vowel, instead of double vowels(noticeably, a very common mistake in non-native speakers).

Most native Japanese teachers will use this system as well, as it uses the proper spelling in terms of sounding out each syllable and vowel individually.
This is the system I use to type romanized Japanese in, and will probably remain so.