I tend to think of my characters through the lenses of my roleplaying background. I look at two sets of opposing factors: virtue/vice and merits/flaws.

Virtues and vices are a good way to broadly define your character. Virtues include Temperance, Hope, Faith and Justice, among others. Vices can include any of the Seven Deadly Sins. Giving your character these two elements should add a bit of imperfection, so long as you stay true to them.

Merits and flaws are more specific. For merits, any attribute that gives your character an advantage over other people: eidetic memory, ambidexterity, being unusually strong or pretty. Flaws are, of course, the opposite: addiction, cowardly, deficiency in a sense, having an embarrassing secret, aloofness. The most important thing I find is to balance the merits and flaws. If your character has a merit that boarders on mythic then give them a flaw that is equally mythic to balance it out.

These things will not only allow you to create imperfect characters, they will also help you create characters that are easy for a reader to identify with.

Just make them like regular people, I guess. Normal, real-world people are imperfect--they're good at some things and terrible at others; they make mistakes; they do things even when they know they shouldn't, they don't do things even when they know they should. Sometimes (often) things don't work out in their favor. And yet they also do good and right things, often when it really matters, and sometimes it works out for them. That's about it, really. *shrug* Maybe other people will have more to say.

~Neshomeh