Querying the same fields for many different values on AppEngine
With Objectify, you have the option to use the "in" operator in a query. Moreover, it becomes clear from the second block of nested loops that you are only looking for the intersection of the two sets of measuredUserIds and standardIds. So, a single statement should do the trick:

public List&lt;StandardScoreDAO&gt; getStandardScores(
        ArrayList&lt;Long&gt; studentIdLongs, ArrayList&lt;Long&gt; standardIdLongs) {
    ObjectifyService.register(StandardScoreDAO.class);
    Objectify ofy = ObjectifyService.begin();

    Iterator&lt;StandardScoreDAO&gt; i = ofy.query(StandardScoreDAO.class)
                    .filter("measuredUserId in", studentIdLongs)
                    .filter("standardId in", standardIdLongs)
                    .iterator();

    List&lt;StandardScoreDAO&gt; ret = new LinkedList&lt;StandardScoreDAO&gt;();

    while (i.hasNext()) {
        ret.add(i.next());
    }

    return ret;
}


If you access a list merely by iteration (and not by random access or by index), and do not know its size on creation, LinkedList might give you a performance benefit.