Gestalt characters are characters that take two character classes at each level. this is described on pages 72-76 of Unearthed Arcana.
At each level the player looks at the two classes and takes the better hit dice, base attack bonus, individual saves, and number of skill points. Skills from both classes are considered class skills for the player and they get the class features from both classes.
This produces characters with a mix of high number of skill points, more life, and better attack bonuses. Characters like this fit the flavor of the ninja inspired theme making characters versatile and each being able to hold their own in combat and out.