For most people, "changing a compiler switch" to get 64-bit builds for iOS is all you need to do. The situations where you need to make changes are the same ones that have existed for years in C, C++, and ObjC applications. In my case, flipping the switch just triggered some compiler warnings regarding ambiguous data types like size_t where I wasn't being specific as to their size. The compiled builds still worked perfectly fine out of the box, but I was able to go in and be more specific or cast when necessary to eliminate those warnings. An application like Infinity Blade 3 (which is the one you mention during the presentation) is fairly complex, maybe they had some native ASM code in there or something.

Link, because I forgot to post it:
http://help.rr.com/HMSFaqs/e_newsgroups_termination.aspx