1. Any of the Total Annihilation series -
Total Annihilation, Supreme Commander, Supreme Commander 2, TA Spring, Planetary Annihilation - anything in that vein, those are just amazing games. It would be tough to choose a favorite, and every single one of them STILL has a community continuing to work on them, sometimes over a decade after they've been abandoned by the developer. That's how you know it's a good series.
2. Company of Heroes series -
Both Company of Heroes 1 and 2 are masterpieces in my opinion. There's an absolute plethora of generic WW1 and WW2 era strategy games, and these just stand out as the best. Company of Heroes 1 was obviously a classic, it defined the genre. Company of Heroes 2 when it came out was...eww. The single player campaign was a joke, apparently insulting to the Russian people it was supposed to be honoring and representing. The two factions (Russia and Germany) were pretty unique, I guess, but the game left a lot to be desired. Well after about 4 years of expansions, new content, new commanders, and balance patches, it's got to be one of the best strategy games of all time. The 5 different factions, British, Russian, American, Oberkommando West, and Wehrmacht are all fantastically unique and interesting in their own way. That each of them has 6 or more commanders to further individualize their factions gives the game almost endless replayability in multiplayer. Rumor has it that the need expansion will add the Japanese, and at that point (with 3 allied factions and 3 axis factions), the game will be truly complete.
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3. Battlezone 1 and 2.
These are games that, even decades after my childhood as ended, I keep coming back to. Very few people even know about them, but they were one of the first attempts to hybridize and successfully combine First Person Shooter with Real Time Strategy, and to do it successfully. Battlezone 1 Remastered is $13 on Steam and Battlezone 2 is essentially freeware, still being worked on by one of the developers over a dozen years after it was released and abandon by the development team. They are both great games and wonderful to play in LAN parties and with friends. Can't recommend them enough.