The most "heat" in the jalapeno is in the ribs and seeds (the white bits). These parts contain the majority of the capsaicin. Clean that bit out of the pepper when preparing it for salsa or whatever. I also cover my hands, with thin produce bags or gloves, when I cut the peppers up to prevent irritating my skin. Nothing worse than touching your face or, even worse, your eyes, after cutting up a jalapeno.
If you are looking to stuff the jalapenos rather than slice them up, try an apple corer to clean the ribs and seeds out.