Science Fiction author Nancy Kress shared an interesting sequence of blog posts earlier this year revealing the fascinating process a short story can take from the inception of the original idea through to final publication. A seat-of-the-pants author, Nancy started with a dry spell, forged through with passion, but found herself 2/3s of the way through the story and in need of an alternate ending. These are three steps she used to work around a wall in her writing to successfully complete and sell the story.
1) Go back to the last place you're excited about the story (in this case, 2/3 of the way through) and toss out everything after that.
2) Think of a different, but still logical, way for a secondary character to act. Secondary characters are, by definition, not as completely delineated as the point-of-view character and so the author has some wiggle room as to how they might behave. Change something major here.
3) Return to your protagonist -- how does he react to this change of behavior in someone important to him? If nothing sparks for you, try different behavior from the secondary character, or perhaps a different character.
How have you pushed through and finished a story that was giving you fits?