I still don't see a manual gearbox available for the new E-class, nor was one available for the W210. That alone would/will send me looking for an E39.
I own both marques, albeit in the late 80's/early 90's time frame. Both marques are awesome, they're similar and different if you know what I mean. The engineering on the W124 is just in a league of its own. I don't know if it's just their stupid North America marketing arms forcing all this luxo-complexity on us but I do hope the quality problems (seemingly resulting mostly from luxo-doodads) are resolved within 5-10 years when I'll be looking to buy another used one 8^().