I tried watching LIE TO ME last night and found it disappointing on a number of levels. One that sticks in my mind this morning is the protag's lack of any real reason to begin an investigation. I know, TV shows have to get into the action quickly, and we're supposed to believe that this man has an instinct for such things. I will let it go.
In my own work, however, I try for a higher standard. I ask myself, "Are my protags justified?" in each step of the mystery. In the first place, there should be cause to suspect murder. That one's usually easy: a knife sticking out of a guy's back is probably not self-inflicted. Then, as they zero in on suspects, I try to be sure I've provided a reason for it: either that suspect has a motive, is acting oddly, or was in the vicinty. A good opportunity for red herrings comes when the sleuth has his own agenda, he doesn't like the guy and therefore focuses on him for personal reasons. But I try to give a plausible explanation of what premise the protags are following.
Here's an example. My protag, Simon, is called in to investigate a death that may be from poison (Tudor era, no autopsy). He learns that X benefited from the man's death, but X was far away at the time of the murder. I want Simon to retrace X's trip so he can discover an important clue to what's going on. BUT I'm aware as the puppeteer in all this that I have to give Simon a good reason to do it. It can't be a whim. In every conclusion that is made, the reader has to agree that it's logical, given the circumstances. If just once the reader thinks, "Where in heck did he come up with that?" you've lost the logic, and it isn't a mystery anymore, it's a fairy tale.