Amazon Neptune is described as 'fast, reliable, fully managed graph database service that makes it easy to build and run applications that work with highly connected datasets'. There are six alternatives to Amazon Neptune for a variety of platforms, including Mac, Windows, Linux, Online / Web-based and BSD. The best alternative is MongoDB, which is free. Other great apps like Amazon Neptune are CouchDB (Free, Open Source), Couchbase (Free), GraphDB (Paid) and MarkLogic (Paid).
MongoDB is a document database with the scalability and flexibility that you want with the querying and indexing that you need MongoDB stores data in flexible, JSON-like documents, meaning fields can vary from document to document and data structure can be changed over...
Apache CouchDB is a distributed, fault-tolerant and schema-free document-oriented database accessible via a RESTful HTTP / JSON API. It includes incremental map / reduce mechanics for queries and keeps data safe with an append-only datastore.
Couchbase is the NoSQL database market share leader, with production deployments at AOL, Deutsche Post, NTT Docomo, Salesforce.com, Turner Broadcasting Systems, Zynga and hundreds of other organizations worldwide.
GraphDB is a RDF graph database or triplestore. It is the only triplestore that can perform semantic inferencing at scale allowing users to create new semantic facts from existing facts. It also has the ability to visualize triples.
MarkLogic is the only Enterprise NoSQL database, bringing all the features you need into one unified system: a document-centric, schema-agnostic, structure-aware, clustered, transactional, secure, database server with built-in search and a full suite of application services.