The Nikon mount is far older than the Canon one. Nikon have updated their old (OLD!) manual focus lens mount continously, adding new mechanical and electronic connections to it over the years to support new features. Canon started with a blank sheet of paper on their EOS mount in the late eighties and did not even try to maintain backwards compatibility. The main difference is that the EOS mount is all-electronic, there is no mechanical linkage whatsoever between camera body and lens. The Nikon mount has a mechanical stopdown linkage and a mechanical autofocus linkage to let an in-camera AF motor drive the AF mechanism in the lens, plus a full set of electronic linkages á la Canon. The consequence is that an old Canon manual-focus lens is now a useless paperweight while any old Nikon manual focus lens can, in principle (there are some gotchas), be mounted and used on the latest and greatest Nikon DSLR.

Also, the Canon mount has a shorter flange distance and a wider opening. The short flange means that there is room for an adapter to fit lenses with other mounts, the wide opening means that making ultra-large aperture lenses like 50mm f/1 and 85mm f/1.2 is possible. Nikon only goes to 50/1.2 and 85/1.4... whether this difference means much in practice is debatable :)