The best option depends on your requirements. Here's a few solutions (I'm assuming you're using Python, since you didn't specify):
If you need to do transactional updates on an entire tree, and you're not going to have more than about 1QPS of sustained updates to any one tree, you can use the built in support for heirarchial storage. When creating an entity, you can pass the "parent" attribute to specify a parent entity or key, and when querying, you can use the .ancestor() method (or 'ANCESTOR IS' in GQL to retrieve all descendants of a given entity.
If you don't need transactional updates, you can replicate the functionality of entity groups without the contention issues (and transaction safety): Add a db.ListProperty(db.Key) to your model called 'ancestors', and populate it with the list of ancestors of the object you're inserting. Then you can easily retrieve everything that's descended from a given ancestor with MyModel.all().filter('ancestors =', parent_key).
If you don't need transactions, and you only care about retrieving the direct children of an entity (not all descendants), use the approach outlined above, but instead of a ListProperty just use a ReferenceProperty to the parent entity. This is known as an Adjacency List.
There are other approaches available, but those three should cover the most common cases.
