I've run a lot of races that are gone now but had great courses, for example Lake County in NE Illinois; and also a lot that are still around but the courses have changed a lot since I last ran them (Las Vegas, St. Louis, Glass City).
But of the ones where the course has been more or less stable for a while:
10. Boston. The truism that most people will run about ten minutes slower on this course then they could run on a "normal" course has held up for at least 30 years since I first heard it. You're asked to climb after your quads have been beaten from continuous descending. It's not unfair, it's just hard.
=5. Chicago. Flat but butt-ugly, plus lots of concrete, broken pavement, patched pavement.
=5. Rocket City, Huntsville, Alabama. Some very minor hills, one nice long stretch with no turns that can be great depending on the wind.
=5. Madison (Wisconsin). Can be warm, but they've managed to take out almost all the hills. Scenic with a lot of variety. Some broken up concrete streets and narrow, winding bike path sections.
=5. Indianapolis ("Monumental", November). Really nice city course, very flat, they have some issues they need to address with private vehicles getting onto the course during the race due to insufficient volunteer force.
=5. Indianapolis (Ft. Benj. Harrison, October). Nice variety, few hills, can get very lonesome after a while if you're doing the full marathon.
4. Amsterdam. Flat, fun, great variety, some streets made of brick pavers which are hard but otherwise OK, great start & finish on 1928 Olympic Stadium track. Uncrowded, by European mega-marathon standards.
3. Lakefront (Milwaukee). Very nice rural first half to suburban second half. Some goofy parts where you're restricted by cones to the most steeply crowned section of the road. Huge downhill about three miles before the finish.
2. Grandma's. Great course for getting into a rhythm, with lots of gentle easy rolling small hills. One big hill late. Very cool finishing stretch.
1. California International. Super-fast and easy on wide, well-maintained roads. Great weather most years.