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

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

var objArr = [];            //定义一个空数组
var len = arr.length;

for (var i = 0;i < len; i++){
    var Id = arr[i].id;
    var Name = arr[i].name;
    var Value = arr[i].value;

    if(!objArr[Id]){        //objArr[Id]未定义或不存在
        objArr[id]  = {};
    }

    if(!objArr[Id][Name]){     //objArr[Id][Name]未定义或不存在
        objArr[Id][Name] = {};
        objArr[Id][Name].Value = [];
    }

    objArr[Id][Name].Value.push(Value);
}

console.log(objArr);