1. Rise of Nations/Thrones & Patriots
I love this game I still play it often, this is what the age of empires games should have been, great depth, excellent meld of turn based meta on the map and real time. So many features like the unit time with change the different bonuses per country, cards with bonuses, etc...a great game.
2. Star Trek Armada II
ONe of the few times I like the sequel more than the original, in particular the simplification of the crew/officer reasource, there was just a bit too much complexity in the economy of the first one for my personal tatstes. One of the only 3D rts out there, an excellent map creation / mod tool allowing for even full mission/senario creation, some of the best unit AI I have ever had the joy of playing with/against, and a good mix of varied races.
3. Dawn of War up to Dark Crusade
Brutality, brought gratuitous violence from fps to rts as well as introduced many new features to the rts market, varible cover, moral ( a favorite mechanic), and a fast paced almost twitch style of forced expanison with its innovative reasource system. Unfortunatly the cameras low ceiling can be frustrating, THQ's support for it (patches, extra content) sux/ non existent, and its sequel took a great start and dumbed it down while slappoing prety graphics on it.
4. Star Wars Empire at War & Forces of Coruption
A veyr fun game to play if a bit exausting with the amount of well managmet involoved; the main thing that drags this lower on the list is the ground portion of the game, maps are very repetive, units not as dynamic as for the space battles.
5. Sins of A solar Empire
Innovative, massive scale
however it does have some major cons that drag ti down for me and I hope to see improved in the future as I beleivce the engine has a lot of potential: Very long game times for the most part, can be a drag would like to see jsut a straight up fleet combat option added like in EOW where you can skip empire building and just smash some heads if in a less patient mood, NO CAMPAGIN AND SHALLOW STORY LINE, a real bummer for me becuase I like immersion in my games, low production value on intro and avatars, fell kinda tacked on and out of place in a game with 3d models to have 2d avatars slaped on, and last but by no means least, the lack of a true 3d implementation for combat and building. A good start, and a good company, but the game fell short for me.
Honorable mentions
Supreme Commander
a good prrof of concept of seemless zoom and various managment tools, but its bugs on relese, lack of difference between factions (there basically all te same with diff paint jobs), and run of the mill storyline ruin what could have been a great succesor to total anhilation.
Starcraft
Good Campaign, fairly good balance, seriously overhyped though
Command and Counquer (entire franchise)
I really enjoy its slick interface and its a good pary game but wish some more depth and strategy would be mixed in