For me, I'd probably break down games by subject matter:
Best Naval Wargame: Harpoon.
Best Air Wargame: Flight Commander 2 (also Over the Reich/Achtung Spitfire)
Best Tactical Wargame: CM Series.
Best Strategic Wargame: TOAW
To me, one of the things that makes them the best is that even though the most recent of them is 7 years old (at least the first iteration), I'm still playing them, if only occasionally for some. (Well, except for Harpoon, but I expect to be buying the Matrix CE version shortly ).
--Philistine