The 2000 Off-Broadway is my favorite, BUT the orchestrations/arrangements are unique to that production alone. This is not the version of the show that is usually performed or even available for liscensing.
If you had to pick a stater recording, I would pick the 1993 London Studio Recording. It's hard to find in stores, but I put a link to it on Amazon below. This recording has all the material (as currently liscensed) without the dated sound of the original recording. Bonus: a young Ruthie Henshall singing 'Turn Back, O Man.' The original would be my second choice though, and then pick up the 2000 Off-Broadway if you find you like the material.
I don't care for the movie soundtrack, and it also lacks a great deal of material (even if it does have the original version of Beautiful City), and the 2001 Touring Cast is, well, kind of embarassing.
GODSPELL 1993 London Studio Cast
...this bird is singing.