To begin, in Hebrew, God's name appears as four consonants: יהוה. These four Hebrew letters are represented in many languages by the letters JHVH or YHWH and are known as the Tetragrammaton.
It is true that no human today can be certain how God's name was originally pronounced in Hebrew because Biblical Hebrew was originally written with only consonants, no vowels. When the language was in everyday use, readers easily provided the proper vowels. However, at some point a superstitious idea arose among the Jews that it was wrong even to pronounce the divine name so they used substitute expressions. Centuries later, copyists kept to following the tradition of eliminating the distinctive name of God by replacing it with Ky´ri·os and The·os´ ("LORD" and "GOD"). Unfortunately, because of the superstitions and traditions concerning the Divine Name, God's name was generally removed from the texts altogether and thus the original pronunciation of the divine name was lost.
Many scholars favor the spelling "Yahweh," but it is uncertain and there is not agreement among them. On the other hand, "Jehovah" is the form of the name that is most readily recognized, because it has been used in *English* for centuries and preserves, equally with other forms, the four consonants of the Hebrew Tetragrammaton.
We can easily understand why many scholars prefer "Yahweh" since it clearly uses the four consonants YHWH. But you wonder why we find so many Bibles using the name which has a "J"?
In the Middle Ages, the "Y" sound of the Greek "I" came to be written as either "I" or "J" (for the first letter of words, at least), and "Iesvs" became either "Iesvs" or, more ornamentally, "Jesvs." And, finally, the "v" came to be written as "u" and the name came into its final written form (in English) as "Jesus." (In fact, even the first editions of the King James Version still used the initial "I" instead of the equivalent "J" which shows that it was still pronounced "Yay-soos" in the English of 1611:
"In form, J was originally merely a [more ornamental] variation of `I,' arising in the 14th century .... Not until the middle of the 17th century did this usage [the new pronunciation of the new letter `J'] become universal in English books; in the King James Bible of 1611, for example, the words Jesus and judge are invariably Iesus and iudge." - p. 4823, Vol. 13, Universal Standard Encyclopedia (Funk & Wagnalls), 1955.
"In the word `hallelujah' the j retains its early consonantal value of i or y." - p. 571, Vol. 15, The Encyclopedia Americana, 1957.
So even for some years after the KJV began using the new letter "J," the pronunciation of it was still "Y." But eventually (18th century?) we began to have "Jesus" (and other "J" words, including "Jehovah," "Jeremiah," "Jerusalem," "Joshua," etc.) with the modern English pronunciation of those letters: "Jee-suz." Nearly all modern English Bibles have purposely retained the earlier tradition concerning biblical names, and "Jesus" (and "Jeremiah," "Jerusalem," "Joshua," etc.) remains in all modern English Bibles.
I believe there is nothing wrong with retaining this tradition even though it is not the original pronunciation of the name of the Messiah (Yehoshua) nor even the original Greek rendering of it (Yaysoos). It is still an honest transliteration of the original proper name of the Messiah, however, and it is common to all speakers of English. (In like manner, although `Cristobal Colon' may be the original pronunciation, I don't think it's wrong to call the famous explorer `Christopher Columbus' in modern English.)
In the same way the only proper name of God Himself, YHWH, which is used nearly 7000 times in the original writings of the Old Testament is sometimes transliterated as "Jehovah" in English (ASV, Young's, KJIIV, NWT, Byington, and, in some verses only, in NEB, MLB, KJV, and Living Bible) and, more rarely, as "Yahweh" (JB, NJB, and Rotherham). (Of course it is more often improperly rendered "LORD" in most places in most Bibles.)
So which is the proper pronunciation of God's name - "Jehovah" or "Yahweh"? Well, many Bible scholars in more recent times have preferred "Yahweh" as the probable original Hebrew pronunciation. But there is still more to say for "Jehovah" in addition to the fact that it is the older, more traditional, and better-known form.
Recommended Articles:
The Divine Name—Its Use and Its Meaning
http://www.jw.org/en/publications/books/bible-teach/the-divine-name-its-use-and-its-meaning/
Should the Name Jehovah Appear in the New Testament?
http://www.jw.org/en/publications/magazines/wp20080801/name-in-new-testament/