Bottom line: a story is probably never good enough. But the real question that needs to be asked is: when is it good enough to get published?
This is something all writers struggle with, from amatuer and professional. The difference is the professional writer has a team of editors and readers who can help with this process. For the rest of us, we need to write and re-write and re-write and re-write . . . all the while relying on no one else but ourselves.
I've been working on Beholder's Eye for several years now (harboring a guess at around 2002 or 2003 when the first draft was written) but it hasn't all been for BE. I wrote a 900-page fantasy epic right afterwards--yes, I went from horror on my first three novels, a thriller on the fourth, and the fifth is fantasy . . . phew!--so my time hasn't been dedicated to this one book. I've also written the beginning bones to about two dozen other novels and several short stories.
But I have come back to it from time to time. Then, in April 2010, our little library in Red Lake Falls was honored to have a literary genius Ian Graham Leask speak on the publishing industry and even took questions from each and every one of us. I asked him about thrillers. He said that thrillers, unlike other genres like fantasy, are typically time-sensitive. He asked me to go back through my thriller and update things to see how "timely" they are. This made a world of difference. In the original drafts, my cops were using paper case files when in fact they're should be using something more modern and digital.
Back to the original question on when a story is good enough for publication . . . is entirely up to other readers and literary agents/editors. Try your story out on a writers' group. Nowadays, I read a story so often until it "sounds" as good as it's going to get, chiseling off all the little bumps from my literary sculpture.
And, if all else fails, try write something else. You should always be writing. Keep in mind, Stephen King didn't publish the first book he wrote either. Carrie was his third.