I am limiting this list to the last 35 years because I want to eliminate engines that would not impress us without "for the time" being added to the sentence. Next, I want to add that reliability is a component as I don't want people naming powerplants that can't reach 60,000 miles.
My short list:
1. GSX-R1100 engine as tuned in the Bandit 1200 - These engines are extremely torquey and are detuned to run forever.
2. SV-650 - These compact and lightweight engines show that you can have torque in a small package.
3. VFR-750 - 100 hp, compact, smooth, and very low maintenance. I view these as what the being what the CB750 4 was relative to the competition in 1969.
4. GPZ-550 - This one is air-cooled, reliable as can be, and had one horsepower for every ten ccs back in 1981.
5. Ninja 250R - This engine that has been used since 1986, can rev to the moon, and has an actual top speed of over 100 mph. This engine (and bike) makes scooters look pointless.
6. GS500 - I am pulling this from the list after realizing that Wiki's quoted horsepower number is 25% higher than every other publication.