I can think of a couple candidates for the 90's easily, but for the 00's nothing immediately comes to mind. What do you think, ESB?
Bute? Cotto? Prolly Bute. He gets a good chunk of his KOs with southpaw lefts to the body, usually either uppercuts or hooks to the liver from southpaw stance.
Although its all but gone today, at 140 Cotto was a very serious body puncher, and was instrumental in his success against Torres, and for one of the best recent (2000's) body punching displays, look no further then Cotto vs Bailey, Bailey gets systematically broken down by an onslaught of precision home run body shots from a vintage cotto. Ward was also a very good body mauler, with probably his most noteworthy coming against Gatti in their first fight, making gatti kneel with a crippling hook to the body when already having thrown everything and the kitchen sink at his head. MAB will be a favorite to list.... and he deserves it. Castillo deserves mention i believe Hatton deserves some mention as well, while its not his staple, he goes to the body well also and it is a part (or was i should say) of his overall presence during the fight.