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The UTK Song Index has this song listed in nine different books in the University of Tennessee Library. The best history I could find is in Best Loved American Folk Songs [Folk Song: U.S.A.], by John and Alan Lomax (1947). Here's what it says:

In its present form, this is a hillbilly blues. However, Woody Guthrie, the Okie balladeer and guitar-picker, learned it from a Negro shoeshine boy in his home town of Okema, Oklahoma. The tune has appeared in many disguises and has relations all over the South. In the tidewater country of Virginia, they call it the "Reuben Blues" and they sing:

REUBEN BLUES

When old Reuben left home, he wasn't but nine days old, When he come back he was a full grown man.
When he come back he was a full grown man.

They got old Reuben down and they took his watch and charm,
It was everything that poor boy had.
It was everything that poor boy had.

In the backwoods, further west, the sharecroppers, white and black, dedicate the tune to a full belly, and sing:
I got my chickens in my sack and the hounds are on my track.
But I'll make it to my shanty 'fore day,
And I'll keep my skillet good and greasy all the time.

Up in Kentucky and Tennessee, they tell the story about a train that ran around a notorious coal mine, where convict labor was used in the old days:
The longest train that I ever seen,
Run around Joe Brown's coal mine,
The engine past (sic) at six o'clock,
And the last car passed by at nine.

Perhaps the oldest of all versions is the Southern mountain song of the dark girl:

Black girl, black girl, don't lie to me,
Where did you stay last night?
In the pines, in the pines, where the sun never shines,
And I shivered where the cold wind blew.

Wherever this melody has turned up, it has been a vehicle for melancholy, for a yearning toward faraway places and toward things that are lost and irretrievable. In "Nine Hundred Miles," it has become the most haunting of railroad blues.

It would be interesting to see how many songs we have in the database that are related to this song by tune or by lyrics.
-Joe Offer-