配列オブジェクトは、あるkeyと同じ組み合わせでグループ化されます.

var arr = [
    {"id":"1001","name":" 1","value":"111"},
    {"id":"1001","name":" 1","value":"11111"},
    {"id":"1002","name":" 2","value":"25462"},
    {"id":"1002","name":" 2","value":"23131"},
    {"id":"1002","name":" 2","value":"2315432"},
    {"id":"1003","name":" 3","value":"333333"}
];

var map = {},
    dest = [];
for(var i = 0; i < arr.length; i++){
    var ai = arr[i];
    if(!map[ai.id]){
        dest.push({
            id: ai.id,
            name: ai.name,
            data: [ai]
        });
        map[ai.id] = ai;
    }else{
        for(var j = 0; j < dest.length; j++){
            var dj = dest[j];
            if(dj.id == ai.id){
                dj.data.push(ai);
                break;
            }
        }
    }
}

console.log(dest);