I'm surprised all of the favorites mentioned are passenger sets. As fond as I am of my Hiawatha and State sets, the AF Brass Piper with a string of AF freight cars is hard to beat. The MTH reproduction is as good looking as the original, and runs well too.
My Waterman Loco Works "GG2" ( fantasy 4-6-6-4 PRR steam locomotive) is in a class by itself. A perfect blend of tinplate style and realism.
Other MESG (modern era standard gauge) trains are also contenders. Who wouldn't like to own a Jerry Brown streamliner?
So many great trains have been made in standard gauge. Picking one favorite is like picking a favorite child!
Kirk