I think the best thing for long distance comfort, especially consecutive days of riding is a good seat. I hated the stocker. It made me antsy after 200 miles. My Rick Meyers seat after about 1000 mile break in/ aquantance was (still is) butt nirvana.
I also learned on my cross country trip that those pricey LD comfort shorts are well worth the money.
+1 on all this: hating the stock seat, butt saved by Rick Mayer, and LD Comfort undies (though like Ms. Kitty, I prefer the tights to the shorts).
But that's butt stuff and you said a few posts later that it was really your back.
For me, riding back pain is pretty strongly correlated with how much time I spend working my abs. Those who have met me would likely say, "He works his abs?!?" Seriously, I'm not going to be asked to pose for muscle magazines, but even light abs work keeps the stress off the lower back.
You might also try the Back-A-Line thing that Patriot posted. I used to wear a Bohn back protector that provided the same kind of support and the difference was notable.