Big trains first (from my working days):
EMD GP38 and GP40 series -- great handlers, smooth riding, responsive throttle. The 38's were great for local freight and yard switching.
EMD SD40 and SD50 -- best over-the-road engines of my time. The 50's on Conrail were nicknamed "the Cadillacs", because that's how they rode. Felt light as a feather, even though they were big. This is 180 degrees from the typical GE locomotive, which rode "like it weighed 400 tons" (hard).
The winner:
Amtrak's (now gone) AEM-7.
The BEST engine I ever worked on.
These (along with the F-40, also a great engine) were the locomotives that saved Amtrak in the early 80's.
On the model railroad:
Walthers Proto SD9:
Smooth!
Atlas C425:
Another smooth runner, picked this up as "new/old stock" through the HO swap list.
Old [Life Like] Proto 2000 GP9:
When I first got this, it ran jerky and the bearings squealed. I changed out the wheelsets, almost required on these because of the "splitting gear problem". I put some oil on the bearings, but it still squealed, so I put it "on the shelf" for about 6 months, wondering what it would take to get it running better. I was going to take it apart, but gave it a quick tryout first, and -- amazingly -- it now runs as well as anything else I have. That oil must have taken its time to get in the proper places!