Well... there are several strategies which Batman can employ to damage and incapacitate superman. How successful he is at these depends on the conditions of their meeting, and thus, are in the hands of the writer.
1) Hypersonics. As stated above there are frequencies which could, conceivably cripple the man of steel due to his superheraring. There are also, in hypersonic theory, frequencies which cause physical damage to tissues that resonate at that frequency. Batman, if he could deduce these two frequencies would be able to cause superman a great deal of pain at a fair large range, perhaps with a relatively small device.
2) Kryptonite. Pretty straightforward. Rings. Batarangs. Kryptonite Gas. Ambient Kryptonite Radiation... Metallo's Kryptonite Lasers... Batman has a number of ways to deploy and employ kryptonite for pain and weaknening of superman. this is a powerful tandem move because, in tandem with other strategies, Superman is constantly getting weaker and more susceptible to other attacks, and he could potentially leave himself open if he tries to deal with the krptonite first. This is to say nothing of other kryptonite colors.
3) Light Flashes. Superman's eyes are suceptible to light attacks. Extremly bright light attacks, perhaps lasers, but still. Similarly, it could be concluded that large bursts of ultraviolet radiation or infrared or x-ray radiation could 'blind' him as well, or at least draw him to shield his eyes. In tandem with sound attacks you can leave Superman senseless and thus, unguarded.
4) Loopholes. There's a ton of them and they're tempting for the writer because they make sense. Eardrums for instance (used by Midnighter on Apollo in Authority: Revolution). Eardrums HAVE to be sensitive so that they can move with sound and the person can ear. Striking a person on their eardrum at sufficient force could burst the eardrum and further deafen the man. Of course, Superman's eardrums have been through worse, so it doesn't work on him, but it technically should. There are many other such cases.
5) Loved Ones. Superman is probably not convinced that Batman won't hurt Lois Lane or Lana Lang. That gives Batman leverage to control and direct superman. Batman can set traps, Batman can hold hostages. Batman can direct and control a situation, if, in the very least, as a distraction. Put civillian in danger around some Kryptonite, and get to kicking butt on a distracted Superman.
6) Large amounts of raw damage. In Hush, Batman dazed Superman with a city power grid. Perhaps feasable. Also if Batman can get his hands on some small nukes (and he can) he could probably hurt the man of steel pretty bad. Now, collateral damage would be an issue, but, if the area is unpopulated, this is doable.
Those are just a few strategies off of the top of my head. Batman has an advantage in that Superman ALWAYS holds back. Period. The problem is of course that Superman is just so dang fast. (I've already shown how his strength can be overcome thoroughly). But honestly, Superman should get the first move and Batman typically wouldn't be able to counter it. Perhaps if the fight started and Superman didn't know where on the Planet Batman was, then Batman would probably be able to pull it off, but then, that underlines pretty amazingly that this isn't a fair fight.
