Coming up with a fresh, new idea for a story is always a challenge. In fact, many writers (myself included) would argue that there are essentially seven basic plots and that every bit of literature from Homer's Iliad to The Dark Knight make use of these archtypes. This doesn't mean that you should give up on the idea of creating something fresh and new, however. It just means that your plot might not be as unique as you thought it was.
The editors at Strange Horizons Fiction have seen their share of overused plots. In fact, they've compiled two lists of these plots for would-be contributers to their e-zine. The first is 'Stories We've Seen too Often' and the second is 'Horror Stories We've Seen too Often'. Both of these lists are an excellent resource and offer a glimpse into the editor's point of view (sometimes a very ellusive thing.)
The point is that if the editors are telling you what they don't want to see, then trust their instincts, not yours. Relying on the hackneyed, the over-used, or the cliched will not help you get published.
Now, if you're out of ideas and feel that your creativity needs a boost, you can visit the Plot Scenario Generator. Maybe a little randomness is just what your story needs!