[nicois]

Is it possible you haven't added the bounding box for your geometries? The GIST index will use your bounding box to optimise the queries, but only if it finds one. Also make sure your query is actually using the index.

[cwmma]

assuming you're using the postgis spatial data types (and not the postgres ones) it'll take care of that automatically.

[nixpulvis]

Yes, I'm currently just using a single PointZ column, which is at least making some use of the index on my relevant 3DDWithin queries.