A simple Illustrator CS5 script to 4-bit align all of the swatches. (Useful for working with RGBA4444 images). Can easily be modified to work with other types of color formats (see the alignment part of alignedColor function).

Align Colors.jsx

var docRef = app.activeDocument;

app.activeDocument.RGB

var alignedColor = function(color, alignment) {
    if (typeof(alignment) == "undefined") {
        alignment = 16;
    }

    var returnColor = (Math.round((color + 1) / alignment) * alignment) - 1;
    if (returnColor < 0) {
        return 0;
    }

    return returnColor;
}

var keys = function(obj) {
    var results = [];
    for (var property in obj) {
        results.push(property);
    }
    return results;
};

var fixSwatchGroup = function(swatchGroup) {
    for (var i = 0, len = swatchGroup.length; i < len; i++) {
        var currentSwatch = swatchGroup[i];
        var rgbColor = currentSwatch.color;
        if (rgbColor.typename == "SpotColor") {
            rgbColor = rgbColor.spot.color;
            if (rgbColor.typename == "RGBColor") {
                rgbColor.red = alignedColor(rgbColor.red, 16);
                rgbColor.green = alignedColor(rgbColor.green, 16);
                rgbColor.blue = alignedColor(rgbColor.blue, 16);
            }
        }
    }
};

fixSwatchGroup(docRef.swatches);