Malcolm Reynolds and his crew live on the edge of the law, preferring to do jobs -- legal or not -- on the outer planets where Alliance influence is weak. Things get sketchy when they unknowingly take on two Alliance fugitives: a doctor and his genius little sister. The Alliance had been secretly experimenting on her, and they desperately want her back.
Half a season, 14 episodes. Fox killed this one partially by airing the episodes out of order. Fortunately Joss Whedon is the leader of an online cult with the motivation and power to finish the series. Though I think all of us would prefer if it never ended.

Brisco County, a Harvard-educated lawyer-turned-bounty hunter, is after the infamous bandit John Bly Gang that murdered his father, Marshal Brisco. It's a western, but with sci-fi and steampunk elements thrown in. Oh yeah, and Bruce Campbell.
Fox (once again) gave up on this one after 27 episodes. Fortunately the secret of John Bly had been revealed by then, but still.

On a date with his wife, photojournalist Thomas Veil returns from the bathroom to discover his life has been erased. Nobody knows who he is, not even his wife. Every trace of his identity is gone. He discovers it's somehow related to a picture he took years before, but he doesn't know why. He must keep the negatives safe from a mysterious organization out to get him, while at the same time trying to learn the truth about what happened to him.
The defunct UPN canceled it after the first season, 25 episodes. Long enough to find out some cool things about Thomas' past. Not long enough to find out what they meant, dang it.

Pirates of Dark Water
Ren, the exiled prince of a sunken kingdom, is charged with finding the 13 Treasures of Rule to stop the ever-hungry Dark Water from consuming the world of Mer. He has an "unlikely but loyal crew of misfits" on his side, but the Pirate Lord Bloth is after him, trying to take the treasures for himself.
This one died on ABC after 20 seasons (although it started on Fox Kids -- a trend?), after Ren had found only eight of the treasures.
All of these shows had hardcore fans and critical acclaim, but they didn't make it. If there's a lesson for writers here, it's that everything's subjective. Though at least in writing, if you have fans and acclaim, you can self publish.
What were your favorite murdered shows?