When asked what the best car he ever made was, Enzo Ferrari replied, 'The one I have not yet built'. Computer hardware and software designers like to say that if it works, it's obsolete. Spacecraft are never cutting-edge in absolute terms because they takes years to get funding, the designers prefer proven components that have been used already, then they take years to build, and years more to fly to their destinations. With that in mind, I'd pick the ones that performed the best in fulfilling their missions. Cassini-Huygens is certainly on my list, as are the Mars rovers for their completeness and the crazy skycrane actually working (once so far, anyway). New Horizons certainly because of its challenges and built-in limitations due to budget.
Definitely disqualified is the James Webb telescope despite its innovative design because of catastrophic mismanagement. I'm sure it will generate great science once it's in place, but I would have cancelled it years ago pour encourager les autres.