Of your favorite movies, are there any that went into obscurity or are generally considered to be bad movies? I'm not talking about "so bad it's good" movies like The Room. You can check the IMDb top 250 list or Rotten Tomatoes to double check.
Mine is Seven Pounds (starring Will Smith, got 27% on RT).
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My first thought was Donnie Darko, but it has developed such a cult following that I don't think it's unpopular anymore.1