For my opinion these are the most usable format for every WebGL applications:
MD2 Quake models format: Introduced in 1997 from ID software for Quake2 game engine. Multitextures supported and skinning animations data. I found some good examples in threejs.org.
Direct3D (.X): This is the Microsoft Direct3D file format basically used in many game engines.
Collada: its been introduced in 2004 and this is multipurpose and versatile format. But unfortunately I hadn't found great examples in threejs.org
Autodesk FBX: developed and owned by Autodesk that's why its supported by all major 3D softwares as Cinema4D, Softimage 3D, Lightwave, Maya and 3D Studio Max.