Scapple on the Mac (and recently also the PC) is one of my favorite programs. Unfortunately, Scapple is not available on the iPad. There are several good alternatives, and MagicalPad uses the special features of the iPad to make enhanced diagrams for visual learning and project organization.

March 5 2014: A fourth good alternative to Scapple on the iPad is Trout. Trout is not only a Scapple work-alike, but it also has versions that run on the Mac, iPhone, and iPad. See this post for a demonstration and review of Trout. Trout is probably the best of the four methods but it has a relatively steep learning curve.