Not all unreliable narrators are villains. Dean Koontz's character, Odd Thomas, is one of the most famous unreliable narrators. Odd Thomas is more hero than villain. There are times when he leaves you wondering. Wonder and questioning are the essence of the unreliable narrator.
With villainy, the unreliable narrator blurs the lines between good and evil through obfuscation, withholding essential truths, outright deception, distracting the reader by espousing views that are repugnant, or being incapacitated in a way that contradicts his or her version of events.
Another way mystery authors accomplish the unreliability of the narrator is to present several versions of the same story from the point of view of different characters. In this version, villainy is depicted through the biases and character flaws of the different points of view. The essential facts remain the same, but each storyteller presents them in a different light. Citizen Kane demonstrates this very well in presenting five varying views of the main character through the eyes of acquaintances. This kind of story leaves us questioning who we should believe.
In mystery, Agatha Christie experimented with the unreliable narrator as a villain in The Murder of Roger Ackroyd and Endless Night. Not being able to trust the narrator of the story was almost unheard of before Christie. In The Murder of Roger Ackroyd, her villain withheld information, obfuscated facts, and evaded answering questions, but never outright lied. Although I enjoyed the story, she was widely criticized for "not playing fair with the readers." Having read the story, as well as all the other Christie books, I can say that she did not play unfairly in presenting the facts. The murder can be solved with the information given, but the controversy serves as a warning to writers today.
Being unfair to the reader is a cardinal sin with mystery readers. If your readers feel cheated by the omission of details, it can damage your reputation as a mystery writer. I'm not trying to warn you away from writing unreliable narrators, though. Excellent mysteries can be and have been written using all states of reliability. Some of the best stories depend on ambiguity and shades of truth to create the desired mood. The real question to consider: are you up to the task of writing this kind of bad boy? If you are planning to use this villain, you must pay attention to presenting all the clues readers need to solve the puzzle.