Implement equals, hashcode in User

    @Override
    public boolean equals(Object obj) {
        if (obj == null)
            return false;
        if (!(obj instanceof User))
            return false;
        User u = (User) obj;
        return this.empCode == null ? false : this.empCode
                .equals(u.empCode);
    }

    @Override
    public int hashCode() {
        return this.empCode == null ? 0 : this.empCode.hashCode();
    }

    @Override
    public String toString() {
        return "Emp Code: " + this.empCode;
    }

Then use retainAll

list2.retainAll(list1);-->EMP01, EMP02, EMP09, EMP10

You can do something like this:

for(User u1 : l1) {
    boolean unique = true;
    for(User u2: l2) { 
        if(u1.getUserEnteredValue().equals(u2.getValueReturnedFromDatabase())) {
            unique = false;
            break;
        }
    } 
    if(unique){
        l3.add(u1);
    }
}

Convert Lists to Collection and use removeAll

    Collection<String> listOne = new ArrayList(Arrays.asList("a","b", "c", "d", "e", "f", "g"));
    Collection<String> listTwo = new ArrayList(Arrays.asList("a","b",  "d", "e", "f", "gg", "h"));


    List<String> sourceList = new ArrayList<String>(listOne);
    List<String> destinationList = new ArrayList<String>(listTwo);


    sourceList.removeAll( listTwo );
    destinationList.removeAll( listOne );



    System.out.println( sourceList );
    System.out.println( destinationList );

Output:

[c, g]
[gg, h]

[EDIT]

other way (more clear)

  Collection<String> list = new ArrayList(Arrays.asList("a","b", "c", "d", "e", "f", "g"));

    List<String> sourceList = new ArrayList<String>(list);
    List<String> destinationList = new ArrayList<String>(list);

    list.add("boo");
    list.remove("b");

    sourceList.removeAll( list );
    list.removeAll( destinationList );


    System.out.println( sourceList );
    System.out.println( list );

Output:

[b]
[boo]

You have already got the Product out of the List<Product> in the following statement:

System.out.println(products.get(i));

Now, that you have got Product, now to get it's id, you can just call it's getId() method:

if (product.get(i).getId() == productId) {
    // Return this product.
}

I would also suggest you to use enhanced for-loop instead of the traditional loop like this:

for (Product product: products) {
    // Now you have the product. Just get the Id
    if (product.getId() == productId) {
        return product;
    }
}

Also, you should change the type of productId from Integer to int. You don't need a wrapper type there.