Creating a JSON Patch document

Alternatively to the approach described in the other answer, you could use the Java API for JSON Processing defined in the JSR 374 (it doesn't use on Gson or Jackson). The following dependencies are required:

<!-- Java API for JSON Processing (API) -->
<dependency>
    <groupId>javax.json</groupId>
    <artifactId>javax.json-api</artifactId>
    <version>1.1.2</version>
</dependency>

<!-- Java API for JSON Processing (implementation) -->
<dependency>
    <groupId>org.glassfish</groupId>
    <artifactId>javax.json</artifactId>
    <version>1.1.2</version>
</dependency>

Then you can create a JSON diff from the JSON documents. It will produce a JSON Patch document as defined in the RFC 6902:

JsonPatch diff = Json.createDiff(source, target);

When applied to the source document, the JSON Patch yields the target document. The JSON Patch can be applied to the source document using:

JsonObject patched = diff.apply(source);

Creating a JSON Merge Patch document

Depending on your needs, you could create a JSON Merge Patch document as defined in the RFC 7396:

JsonMergePatch mergeDiff = Json.createMergeDiff(source, target);

When applied to the source document, the JSON Merge Patch yields the target document. To patch the source, use:

JsonValue patched = mergeDiff.apply(source);

Pretty printing JSON documents

To pretty print the JSON documents, you can use:

System.out.println(format(diff.toJsonArray()));
System.out.println(format(mergeDiff.toJsonValue()));

public static String format(JsonValue json) {
    StringWriter stringWriter = new StringWriter();
    prettyPrint(json, stringWriter);
    return stringWriter.toString();
}

public static void prettyPrint(JsonValue json, Writer writer) {
    Map<String, Object> config =
            Collections.singletonMap(JsonGenerator.PRETTY_PRINTING, true);
    JsonWriterFactory writerFactory = Json.createWriterFactory(config);
    try (JsonWriter jsonWriter = writerFactory.createWriter(writer)) {
        jsonWriter.write(json);
    }
}

Example

Consider the following JSON documents:

{
  "name": {
    "first": "John",
    "last": "Doe"
  },
  "address": null,
  "birthday": "1980-01-01",
  "company": "Acme",
  "occupation": "Software engineer",
  "phones": [
    {
      "number": "000000000",
      "type": "home"
    },
    {
      "number": "999999999",
      "type": "mobile"
    }
  ]
}

{
  "name": {
    "first": "Jane",
    "last": "Doe",
    "nickname": "Jenny"
  },
  "birthday": "1990-01-01",
  "occupation": null,
  "phones": [
    {
      "number": "111111111",
      "type": "mobile"
    }
  ],
  "favorite": true,
  "groups": [
    "close-friends",
    "gym"
  ]
}

And the following code to produce a JSON Patch:

JsonValue source = Json.createReader(new StringReader(leftJson)).readValue();
JsonValue target = Json.createReader(new StringReader(rightJson)).readValue();

JsonPatch diff = Json.createDiff(source.asJsonObject(), target.asJsonObject());
System.out.println(format(diff.toJsonArray()));

It will produce the following output:

[
    {
        "op": "replace",
        "path": "/name/first",
        "value": "Jane"
    },
    {
        "op": "add",
        "path": "/name/nickname",
        "value": "Jenny"
    },
    {
        "op": "remove",
        "path": "/address"
    },
    {
        "op": "replace",
        "path": "/birthday",
        "value": "1990-01-01"
    },
    {
        "op": "remove",
        "path": "/company"
    },
    {
        "op": "replace",
        "path": "/occupation",
        "value": null
    },
    {
        "op": "replace",
        "path": "/phones/1/number",
        "value": "111111111"
    },
    {
        "op": "remove",
        "path": "/phones/0"
    },
    {
        "op": "add",
        "path": "/favorite",
        "value": true
    },
    {
        "op": "add",
        "path": "/groups",
        "value": [
            "close-friends",
            "gym"
        ]
    }
]

Now consider the following code to produce a JSON Merge Patch:

JsonValue source = Json.createReader(new StringReader(leftJson)).readValue();
JsonValue target = Json.createReader(new StringReader(rightJson)).readValue();

JsonMergePatch mergeDiff = Json.createMergeDiff(source, target);
System.out.println(format(mergeDiff.toJsonValue()));

It will produce the following output:

{
    "name": {
        "first": "Jane",
        "nickname": "Jenny"
    },
    "address": null,
    "birthday": "1990-01-01",
    "company": null,
    "occupation": null,
    "phones": [
        {
            "number": "111111111",
            "type": "mobile"
        }
    ],
    "favorite": true,
    "groups": [
        "close-friends",
        "gym"
    ]
}

Different results when applying the patches

When the patch document is applied, the results are slightly different for the approaches described above. Consider the following code that applies JSON Patch to a document:

JsonPatch diff = ...
JsonValue patched = diff.apply(source.asJsonObject());
System.out.println(format(patched));

It produces:

{
    "name": {
        "first": "Jane",
        "last": "Doe",
        "nickname": "Jenny"
    },
    "birthday": "1990-01-01",
    "occupation": null,
    "phones": [
        {
            "number": "111111111",
            "type": "mobile"
        }
    ],
    "favorite": true,
    "groups": [
        "close-friends",
        "gym"
    ]
}

Now consider the following code that applies JSON Merge Patch to a document:

JsonMergePatch mergeDiff = ...
JsonValue patched = mergeDiff.apply(source);
System.out.println(format(patched));

It produces:

{
    "name": {
        "first": "Jane",
        "last": "Doe",
        "nickname": "Jenny"
    },
    "birthday": "1990-01-01",
    "phones": [
        {
            "number": "111111111",
            "type": "mobile"
        }
    ],
    "favorite": true,
    "groups": [
        "close-friends",
        "gym"
    ]
}

In the first example, the occupation property is null. In the second example, it's omitted. It's due to the null semantics on JSON Merge Patch. From the RFC 7396:

If the target does contain the member, the value is replaced. Null values in the merge patch are given special meaning to indicate the removal of existing values in the target. [...]

This design means that merge patch documents are suitable for describing modifications to JSON documents that primarily use objects for their structure and do not make use of explicit null values. The merge patch format is not appropriate for all JSON syntaxes.

As a general architectural point, I usually advise against letting dependencies on a particular serialization format bleed out beyond your storage/networking layer; thus, I'd first recommend that you consider testing equality between your own application objects rather than their JSON manifestations.

Having said that, I'm currently a big fan of Jackson which my quick read of their ObjectNode.equals() implementation suggests does the set membership comparison that you want:

public boolean equals(Object o)
{
    if (o == this) return true;
    if (o == null) return false;
    if (o.getClass() != getClass()) {
        return false;
    }
    ObjectNode other = (ObjectNode) o;
    if (other.size() != size()) {
        return false;
    }
    if (_children != null) {
        for (Map.Entry<String, JsonNode> en : _children.entrySet()) {
            String key = en.getKey();
            JsonNode value = en.getValue();

            JsonNode otherValue = other.get(key);

            if (otherValue == null || !otherValue.equals(value)) {
                return false;
            }
        }
    }
    return true;
}

I've done good experience with JSONAssert.

import org.junit.Test;
import org.apache.commons.io.FileUtils;
import org.skyscreamer.jsonassert.JSONAssert;
import org.skyscreamer.jsonassert.JSONCompareMode;

... 
@Test
public void myTest() {
  String expectedJson = FileUtils.readFileToString("/expectedFile");
  String actualJson = FileUtils.readFileToString("/actualFile");
  JSONAssert.assertEquals(expectedJson, actualJson, JSONCompareMode.STRICT);
}
... 

I did some research to finalise a diff generation library for myself. The bug pointed out by @pacoverflow seems resolved. I did not face this issue. My vote is for fge json-patch because of following reasons:

1. Good documentation support.
2. Supports serialisation.
3. Most closely follows RFC 6902 standards. zjsonpatch may behave different with int and float value comparison (treating 1 and 1.0 different).
4. Open bugs with zjsonpatch indicate possibility of broken patches.