Well, all source ports use the same WADs as the DOS version (that’s a prerequisite for copyright reasons). However, it’s true that some of them ship with additional WADs or PK3s containing new resources.
I prefer MBF in DOS, for the higher resolution and the limit removal.
Doom64 was eventually ported to PC, and then a remastered version was released.
The PowerPoint remake is awesome. It’s not really a port, but merely an interactive PowerPoint game using Doom assets. The amount of work the author has put into it is impressive.