I might vote for Third Age: Total War again. 3.0 is coming and it's still very popular. Voted for FH2 last year.
Republic at War for Empire at War/Forces op Corruption is quite unstable, I only touched a bit of it and got bored, but the guy deserves a mention at least. Did Desert Combat ever win it for BF1942? I played that a LOT. It also had a catchy fan-made rap song but I can't find it anymore unfortunately.