I have two Wolfenstein 3D's right next to each other in my collection. They appear to be the same version 1.4 but one is 12MB and the other is 18MB. The only other difference is one has a link to the "Store Page & Reviews" and the other has "Changelog" in the dropdown.

The smaller version is the old Wolf 3D, the bigger one is the newer version that has the main game and Spear of Destiny bundled but is missing the Return to Danger and Ultimate Challenge mission packs. Those are only included in the old Spear of Destiny.