It may sound Victorian, but I like to hear either "now, now" or "there now."  I've actually said the latter a couple of times, but only to children.

For more modern alternatives, I like either "shhh" (as in, gently hushing someone) or something like "that's right, get it all out."  For whatever reason I'm not a big fan of "It's okay" and the like, which strike me as sort of feeble.

I know this thread is old, but I thought I'd toss my two cents in. Unfortunately, I have never got the amazing opportunity to comfort someone having a good cry. But when I imagine myself doing it, I always think of myself saying "shh", "there there now", "I gotcha", and, my personal favorite, "You're safe in my arms."