Personally, I'd also recommend Homeworld and the Warhammer 40K: Dawn of War series
On the free-and-open-source front there is Zero-K (which I don't care for) and Beyond All Reason, both of these are Spring Engine games, and Spring Engine started out as a 'modernization' of Total Annihilation. Most games built with it don't fall too far from the original
Homeworld 3 comes out in May, I can't wait :D :D :D
ps- I'd be remiss to omit Command & Conquer... Red Alert 2 and Generals are my favorites. I don't care for Starcraft but that series is worth mentioning too.