One obvious difference (which has always been disappointing to me) was the lack of accompanying illustrations to the articles. This line covers their legal liability, if their is any, or this aspect of the CD, I suppose.
Of course, I can buy a lot of archival discs of other publications that are in .pdf format, fully searchable, copy and pastable. But the WTBS never does things the logical way. And why still on CD? DVD hold many times more, they could get the entire print run, Rutherford's Rainbow, Russell's works, and, oh, uh, never mind....