Though I have tried out a variety of 3D mesh-editing programs over the years, the only one that I have found intuitive enough to actually use is MilkShape3D. However, MilkShape3D is Windows-only, and is not Free/Open Source Software. There is a MilkShape-esque program called MisfitModel3D available under a GPL v2 licence, but it doesn't appear to be under active development any more.
I have therefore begun work on my own program, MilkMaid3D, taking inspiration from the simplicity and usability of the MilkShape3D user interface and the direct, hands-on way in which it allows the user to adjust every vertex, triangle and joint manually.
There aren't many "editing" features right now:
The following list contains all of the file formats that are/will be supported by the program.
Yes means that the file format is completely supported.
No means that the file format is not supported.
WIP means that the file format doesn't work yet, but is currently being worked on.
TODO means that the file format doesn't work yet, but it will do at some point.
Entries in Yellow mean "supported, but missing feature XYZ".
I'll be adding more formats (such as LWO) as the project progresses.
*Quake 1 Beta models may or may not be supported at some point. Half-Life MDLs probably won't be.
Compiling and/or Running on Windows
You can download most of the necessary files from the official GTK website.
You can download the development and DLL files for GtkGLExt here.