This site uses the the Kougouyaku Translation (Colloquial Translation) of the Bible to study Japanese. Basically, you can view each book chapter (currently only the Gospel of John) in three columns – an English translation, Japanese with furigana and Japanese without furigana. You can even hide the English column for enhanced study effort.
The site also features a weekly grammar example taken from the reading material and Kanji/Vocabulary flashcards for use in the JFC (Japanese Flash Card) program.
And, for those interesting in Christianity in general, there are many Japanese Christian links.