I find this thread interesting because my first reaction was similar to Marco's. Upon further consideration, as Springsteen's music has gotten darker over the years, I can see where it's starting to approach Waits' sandbox(at least lyrically). In that way, they are plying the same territory. Musically, IMHO, the best you can say is that both are rooted in the blues which occassionally allows for some overlap.
To me, the biggest difference is that Springsteen is literal (both musically and lyrically) where Waits is more fantasical (word advisedly chosen to reference the literary genre). Waits' musical style abstracts traditional rock vocabularly while Sprinsteen's celebrates it. Waits' lyrical style takes dark tales of America toward the surreal, rather than Sprinsteen's real.
I'll take Waits, but I'll also take TC Boyle over Richard Russo - not necessarily the first alternatives you might pair, but not unlike the one posed by this thread and, IMHO, not unreasonable. My taste runs toward the more obviously "imaginative" take on certain common themes, but I also understand why some folks would go the other way.
Marty