To handle the click events you need to run the clickable option to true. Then you can monitor ProtoChart:plotclick event on the chart DIV. You can learn more about Event Handling via Prototype JS site.
var options = {
xaxis: {min: 0, max: 15},
yaxis: {min: 0, max: 15},
lines: {show: true},
bars: {show: false},
points: {show: true},
mouse: {track:true},
grid: {clickable: true}
};
var d1 = [[0,0]];
var graph = new Proto.Chart($('placeholder'), [d1], options);
$('placeholder').observe('ProtoChart:plotclick', function(event){
var position = event.memo[0];
d1.push([position.x, position.y]);
d1 = d1.sort(function(a, b){ return a[0] - b[0]; });
graph = new Proto.Chart($('placeholder'), [d1], options);
});