Right off the top of my head, I can think of 3 times where Superman and Batman have fought in the comics. Twice, Batman went in spoiling for a fight, and came away with a victory...though he didn't necessarilly win the fight.
1. In the Hush series, he went to Metropolis expecting to fight Superman. But he also had no intention of actually fighting him, even the Kryptonite ring was intended just to slow Superman down. Batman's gadgets and prep gave him the ability to avoid most of the direct conflict and slow Superman down early on, but nothing he did was capable of actually stopping Superman, in the end it was only Superman breaking out of Ivy's control that ended the fight.
2. Dark Knight. I haven't read this one as thoroughly as the others, but the whole book was really written as a "Look how uber skilled and talented Batman is. Nothing can stop him for long." So...yeah, of course he wins.
The third...the fight was unexpected....and Batman didn't fare as well.
3. During Infinite Crisis, Max Lord sent Superman to crush Batman. And...he did. Blew through everything Bat's could throw up (including the JLA watchtower security systems) and would have killed Batman, at close range by strangulation, had the other Justice Leagers not arrived in time. This is really the most "real" of the fight scenarios since it's the only one in which Superman wasn't trying to hold back at all.
I do prefer Batman to Superman, but in a fight where the only way to win is to incapacitate the opponent, Batman's only gonna be able to pull off the win maybe 1 in 100 times. The other 99, he's gonna be a little baggie of skin and broken bones. (For which Superman will feel horrible about afterward..)