The studio version is by far my favorite, bittersweet and brooding. Just his angelic voice and a melancholic electric guitar. Listen here:
And one more, live in studio. Great to watch him perform, but it's not quite up to the same level as the album version posted above.

"Hallelujah" has been covered many times by many musicians since and will be covered again, but I don't see how anyone could top Jeff's perfect version. And if you don't have his album Grace, buy it now.