Salesforce: QueryResult must start with '{'

The problem isn't actually that you specify Parent__r. Rather it is that your Parent__r value specifies Children__r as a List<SObject>.

Serialize a query result which includes a Left Outer Join and look more closely. The child relationship key doesn't point to a List<SObject>. It points to a Map<String, Object>. That map must specify both totalSize and done in addition to records.

Won't work:

{
    "Children__r": [{
        "SomeField": "some value"
    }, {
        "SomeField": "some value"
    }]
}

Will work:

{
    "Children__r": {
        "totalSize": 123,
        "done": true,
        "records": [{
            "SomeField": "some value"
        }, {
            "SomeField": "some value"
        }
    }
}

A little late to the game, but for anybody finding this thread, I ran accross the same error, because the retrieval of a subquery through a @RemoteAction produces the incorrect structure as Adrian states:

{
  "Children__r": [{
    "SomeField": "some value"
  }, {
    "SomeField": "some value"
  }]
}

Therefore, if you are using this javascript object to Apex for deserialization through another @RemoteAction, you can "rewrite" it using a javascript function before sending it off:

function rewriteSubquery(array) {
    if (array && !array.hasOwnProperty('records')) {
        var tempArray = array;
        array = {
            totalSize: tempArray.length,
            done: true,
            records: tempArray
        }
    }
    return array;
};

As an example, if you have an object stored in Javascript, with the following structure:

parentObject = {
    Id: 'a0K0E000002AolHUAS',
    Name: 'Test',
    SubqueryObjects__r: []
}

You can then call the method like this:

parentObject.SubqueryObjects__r = rewriteSubquery(parentObject.SubqueryObjects__r);

Which will return the structure that you need for correct deserialization:

parentObject = {
    Id: 'a0K0E000002AolHUAS',
    Name: 'Test',
    SubqueryObjects__r: {
        totalSize: <array_size>
        done: true,
        records: []
    }
}