Nested JSON objects - do I have to use arrays for everything?

You don't need to use arrays.

JSON values can be arrays, objects, or primitives (numbers or strings).

You can write JSON like this:

{ 
    "stuff": {
        "onetype": [
            {"id":1,"name":"John Doe"},
            {"id":2,"name":"Don Joeh"}
        ],
        "othertype": {"id":2,"company":"ACME"}
    }, 
    "otherstuff": {
        "thing": [[1,42],[2,2]]
     }
}

You can use it like this:

obj.stuff.onetype[0].id
obj.stuff.othertype.id
obj.otherstuff.thing[0][1]  //thing is a nested array or a 2-by-2 matrix.
                            //I'm not sure whether you intended to do that.

Every object has to be named inside the parent object:

{ "data": {
    "stuff": {
        "onetype": [
            { "id": 1, "name": "" },
            { "id": 2, "name": "" }
        ],
        "othertype": [
            { "id": 2, "xyz": [-2, 0, 2], "n": "Crab Nebula", "t": 0, "c": 0, "d": 5 }
        ]
    },
    "otherstuff": {
        "thing":
            [[1, 42], [2, 2]]
    }
  }
}

So you cant declare an object like this:

var obj = {property1, property2};

It has to be

var obj = {property1: 'value', property2: 'value'};