The first problem is how to fit them into a DOS/Windows centric environment, which allows chain-loading different types of executables. Actually, from command line, there are two different ways to load a new executable: 1) chain in same process 2) create new console and process and run them there (spawn). The first way will not be supported by 64-bit executables, primary because 64-bit needs a special 64-bit process, and secondary because everything below 4G in a 64-bit process is inaccessible from user-mode (that's why I needed the medium memory model).
Thus, the first thing would be to make the command-shell recognize 64-bit applications (this is done with a new syscall), and then always spawn them regardless of how they are invoked.
The next thing is to check for 64-bit executables in the spawn function (same syscall as above), and create a 64-bit process instead, and also skip a few steps there.
Edit: In segmented designs it is easy to get to a specific position simply by loading a fixed selector, and using it 0-based. The same doesn't work so well in flat mode, and often needs relocation. But for 64-bit an interesting alternative is to use the first linear page, especially since it is not accessible to applications anyway. So by loading the flat selector to ds, and using 0-based addresses, I can address the exact same locations from both protected mode and long mode without using index / base registers. I'll put the executable info at linear position 0, and let it reference pointers in the low 3G address space.