Babylon.js loads .babylon files by default, and this is a JSON format file as described under Further Reading below. Scenes can be loaded and appended. Meshes can be imported directlty or incrementally.
You can also write your own loader for other file formats. Three such loaders one for .obj files, one for .stl files and one for .glTF files have already been written and can be added to babylon.js as extensions.
In order to help developers load multiple assets, there is an assetManager.
Playground Example Import Mesh -
STL
OBJ
glTF
Incremental Loading
Creating Your Own File Importer
Loading Files with Assests Manager