Whether you choose the first or the third option depends on your use case. If you are modeling many different instances of the same type of thing, choose the first. For example, you have a list of people. If you are modeling many different attributes of one thing, choose the third. You can have repeated keys in the first format, but not in the third.

The second option is terrible, and I've yet to find an appropriate use case for it. The reason it's terrible, in addition to being more verbose, is that for single-level JSON, it breaks most libraries' automatic conversion to a dictionary/map. For deeply-nested JSON, it breaks the XPath-like query interface.

This makes it a pain to work with. And if you don't know your keys at compile time, you will want a dictionary or XPath interface, because you won't be able to convert it to a class. It may not seem like a big deal now, but the longer you have a data format, the harder it will be to change.

The library is chained, so you can create your object by first creating a json array, then creating the individual objects and adding them one at a time to the array, like so:

new JSONArray()
    .put(new JSONObject()
            .put("name", "cases")
            .put("value", 23))
    .put(new JSONObject()
            .put("name", "revenue")
            .put("value", 34))
    .put(new JSONObject()
            .put("name", "1D5")
            .put("value", 56))
    .put(new JSONObject()
            .put("name", "diag")
            .put("value", 14))
    .toString();

Once you have the final array, call toString on it to get the output.

Assuming the objects in jsonArray always contain exactly one key, the following should print the key and value in each object as you would like:

for (int i = 0; i < jsonArray.length(); i++) {
    JSONObject jsonObject = jsonArray.getJSONObject(i);
    Iterator<String> keys = jsonObject.keys();
    String key = keys.next();
    Object value = jsonObject.get(key);
    System.out.println(key);
    System.out.println(value);
}

However, you may want to handle all the keys of all the objects by wrapping each key and value in a while (keys.hasNext()) iterator loop:

for (int i = 0; i < jsonArray.length(); i++) {
    JSONObject jsonObject = jsonArray.getJSONObject(i);
    Iterator<String> keys = jsonObject.keys();
    while (keys.hasNext()) {
        String key = keys.next();
        Object value = jsonObject.get(key);
        System.out.println(key);
        System.out.println(value);
    }
}

With your example, both solutions have the same output, but obviously the latter is more flexible.

So why don't you simply use a key-value literal?

var params = {
    'slide0001.html': 'Looking Ahead',
    'slide0002.html': 'Forecase',
    ...
};

return params['slide0001.html']; // returns: Looking Ahead

To parse array inside JSONObject you have to check value instance of JSONArray and recursively call printJsonObject for each array item:

public static void printJsonObject(JSONObject jsonObj) {
    for (Object key : jsonObj.keySet()) {
        Object value = jsonObj.get(key);

        if (value instanceof JSONObject)
            printJsonObject((JSONObject)value);
        else if (value instanceof JSONArray)
            ((JSONArray)value).forEach(obj -> printJsonObject((JSONObject)obj));
        else
            System.out.println(key + ", " + value);
    }
}