(Recently, my 7th level rogue started a combat without his weapons. Rather than spend a turn retrieving them, he started punching opponents with his fists, since the sneak attack damage is most of the damage he does, regardless of his weapons.)
Well unless your rogue has unarmed strike the sneak attack damage done via an unarmed strike (or using a sap) is non-lethal damage.
PHb pg 50
With a sap (blackjack) or an unarmed strike, a rogue can make a sneak attack that deals nonlethal damage instead of lethal damage. She cannot use a weapon that deals lethal damage to deal nonlethal damage in a sneak attack, not even with the -4 penalty, because she must make optimal use of her weapon in order to execute a senak attack.