In my opinion, these are the most important factors in any character design: color, concept, shape, simplicity, cohesiveness, repeatability, personality and uniqueness.
Color: Any design with colors all over the place creates too many places for the eye to look. Keep your color design very simple and zen. Looking at the colors shouldn't be jarring or confusing. This isn't to say only use one color, not at all, but try to make sure the ones you use are harmonious. Avoid mixing and matching different saturations of the same color or picking colors that clash with one another.
My rule of thumb: Stick to no more than three base colors and some value variations.
Concept: Your design should have inspiration, even if the inspiration is just your intended character's personality or an interesting object that represents them. Your character could be a bookworm, and that would impact her posture, her clothing, her hairstyle...pretty much everything about her! You can design clothing based on objects, elements, existing fashions or other things that relate to your character's personality.
My rule of thumb: Your whole design should radiate with one strong idea.
Shape: Every character should have a unique overall shape. Nothing is more boring than a lineup of characters with the same exact body type, height, stance, etc. There's so much that can be conveyed by body shape and posture, and it's really worth looking at pictures of people to learn to draw as many different types as possible.
My rule of thumb: You should be able to recognize your character as a silhouette only.
Simplicity: Even in designs with lot of detail, I think the best character and clothing designs need to be relatively simple in the breakdown. Posture and pose can usually be conveyed in a few lines, and clothing shouldn't have too many elements or pieces to avoid confusing the eye.
My rule of thumb: You should be able to convey your character's overall design in ten pen strokes or less.
Cohesiveness: This goes for every facet of the design (concept, color, shape, etc.) Try to repeat colors, shapes, designs, patterns and overall ideas across your figure. Even if it's something really small, like your character has bright blue eyes, try to repeat a variation of that blue somewhere on the figure - maybe even an accessory or a fringe. Try to use every color and shape more than once.
My rule of thumb: The bottom half of your design should look like it belongs to the top half.
Repeatability: When you design a character, make sure that drawing him/her over and over would not get tedious, or that it would even be possible. Draw him/her from several different angles. Don't include any laboriously detailed patterns or tattoos that would be impossible to draw the same way twice.
My rule of thumb: Drawing your character should be relatively easy.
Personality: Your character's face, stance, clothing choices, even their color scheme should reflect their personality. If you can't hint at their personality through one aspect, double your efforts on the others; for example, if you have to draw a depressed man as a brightly colored clown, make him really slouched, his expression REALLY sour, etc.
My rule of thumb: We should know your character the moment we look at him.
Uniqueness: Perhaps most important of all, your character should be unique in body type, face shape, facial features, posture, deformities, etc. Don't just use one design or shape for everything, even if you really, really like the way one particular thing looks. Hairstyle, accessories and clothing don't count for this category because those things can be changed; don't depend on them to differentiate your character from another! Your character is an individual, so do them a favor and make them look like one. =p
Things to vary on the face include jawline, eyebrows, eye shape and size, nose shape and size, cheekbone placement, lip and mouth shape, ear size and shape, overall placement of the features, hairline, forehead size, and unique features such as scars, piercings and tattoos.
Things to vary on the body include height, weight, posture, skin tone, shoulder width, muscle tone, butt size, arm/leg length and shape, missing limbs, breast size, shape and placement, neck length and torso-to-leg ratio.
For a good example of this, look at the show Avatar; it has characters that periodically change clothes and hair, or are dressed in practically identical clothes, yet you can still recognize them all as individuals.
My rule of thumb: You should still be able to recognize your character even if they were bald and naked.