I'm an SY at Duke and worked in a nonprofit before coming to school. I think that if you're good, you can turn almost any nonprofit experience into a good bschool-app-worthy story. I'll discuss this a little more below, but the first thing I'd say is work someplace that turns you on. It's hard hard work and if you aren't driven from the inside to get up every day, then it's not going to be worth it to you. Do you have anything that you're interested in doing? Technology? Education? Housing? Environment? What "causes" are you willing to put yourself into?
Once you decide what to do, there are some pros to working in np:
you get to management level quicker
you have p/l responsibility fairly early
they're usually smaller, and you get to do more stuff
if you're there, it's because you love it
usually your coworkers love it too
the work you do matters
Bschools like np backgrounds because of the above, and because you're probably a joiner and a contributor. You're unique, both in your background and what you bring to a class discussion - how you think, what matters to you - will be quite different from that of your classmates.
Of course, there are some down-sides too.
NPs have a reputation for being poorly run, and it can be really stressful. You're probably overworked and under-paid. You won't have resources. And the work is just d@mn hard. No one knows what the answers are. Forprofit folks can say, "yep, I sold X widgets and made Y on each one, so our bottom line is Z." Not so clear for the do-gooders. It's hard to know what works, hard to prove you're the best place to put a funder's dollar.
From the bschool side, the adcoms might think that you can't hack "business stuff" like statistics and accounting. They might also think it'd be hard to employ you.
I'm happy to talk about more of this stuff with you, and give you some ideas about the different kinds of nonprofits and what they pay if you give me an idea of what you're specifically interested in.