Robert Bauserman of the Maryland Department of Health and Mental Hygiene in a Meta Analysis examined 33 studies that looked at 1,846 sole-custody and 814 joint-custody children, as well as kids in 251 intact families.  Children in joint-custody settings have fewer behavioural and emotional problems, have higher self-esteem, and better family relations and better school performance than children in sole custody (usually with the mother). Moreover, the bulk of the studies show that children in joint-custody arrangements are virtually as well adjusted as those in the intact families, "probably because joint custody provides the child with an opportunity to have ongoing contact with both parents."

Source

Bauserman R. (2002 Child Adjustment in Joint-Custody Versus Sole-Custody Arrangements: A Meta-Analytic Review. Journal of Family Psychology 16(1): 91-102