HighCharts : Is it possible to customize the colors of individual series?

Options can be set separately for each series.

var chart = new Highcharts.Chart({
    chart: {
        renderTo: 'container'
    },
    xAxis: {
        type: 'datetime'
    },

    series: [{
        name: 'John',
        color: '#0066FF',
        dashStyle: 'ShortDash',
        data: [
            [Date.UTC(2010, 0, 1), 29.9],
            [Date.UTC(2010, 2, 1), 71.5],
            [Date.UTC(2010, 3, 1), 106.4]
        ]
    },{
        name: 'Mary',
        color: '#FF0000',
        data: [
            [Date.UTC(2010, 0, 1), 60.9],
            [Date.UTC(2010, 1, 1), 40.5],
            [Date.UTC(2010, 2, 1), 90.0],
            [Date.UTC(2010, 3, 1), 80.4]
        ]
    }]
});

JsFiddle Example

If you read the api here, you'll see the following text.

Serie

The actual series to append to the chart. In addition to the members listed below, any member of the plotOptions for that specific type of plot can be added to a series individually. For example, even though a general lineWidth is specified in plotOptions.series, an individual lineWidth can be specified for each series.

So you can add anything from plotOptions.

Demo:

series: [{
    name: 'serie1',
    data: [0,1,2,3,4,5,6,7,8,9],
    color: '#FFFF00',
    lineWidth: 4,
    id: 'serie1',
    step: true
}]

Working demo