set different colors for each column in highcharts

Here is another solution with the latest version of Highcharts (currently 3.0).

Set the colorByPoint option to true and define the color sequence that you want.

options = {
    chart: {...},
    plotOptions: {
        column: {
            colorByPoint: true
        }
    },
    colors: [
        '#ff0000',
        '#00ff00',
        '#0000ff'
    ]
}

Here is an example based upon Highcharts Column with rotated labels demo

When you add the value to the series.data you can also set the color using the point options e.g

series.data.push({ y: parseInt(Data[i]), color: '#FF0000' });

For more details about the point options see https://api.highcharts.com/class-reference/Highcharts.Point#color