Here's my big ass list of RTS games. Note: no Turn based games are on this list. And the comments are my opinions. If you know any RTS games that have base building, economy and combat that aren't on the list, please PM them to me.

Enjoy:
This is a list of top down games that focus on base building, economy and combat to varying degrees
This list is bias towards games I like, games which fit the criteria but suck(IMO), are in a second list below.
RTS Games:
Starcraft(1 and 2)
Warcraft series(1, 2, 3)
The Dune games(Dune II, Dune 200, Emperor: battle for dune)
Fuck tonnes of CnC games.(I?m seriously not going to list them all here, go wiki them)
The Homeworld games(especially cataclysm, which is IMO the pinnacle of the series)
Rise of nations(a sort of real time mix of Civilisation and an RTS)
Total annihilation and Supreme commander(Supreme commander 1 > supcom 2)
Lego Rock raiders(no joke, this game is old, but awesome)
Age of empires 1/2
Age of empires Online(the MMO crap is kind of annoying, but their's a very solid age of empires game hidden within, very similar to the first two age of games)
Age of mythology( one of, if not the, best age of empires games)
Battle for middle earth(the first one, number 2 breaks all the things they got right with the first one)
Outpost 2(old game that focus' on base management and research, hard to play due to really outdated interface, but still pretty cool)
The Settlers games(specifically 3 & 4)
ANNO 1404(and other anno games, a Good mix of city building and naval combat, forcus' mainly on economy and city building)
ANNO 2070(same pros as Anno 1404, with some more advanced community and multiplayer features)
Dawn of War(1 and it?s expansions, DoW2 is more of a tactics game)
Games I haven't played(but want too):
CnC 4(I'm pretty sure it's bad, but I'm naive enough to withhold judgement until I've played it for myself
Age of Empires 3
Metal Fatigue
The Moon Project
Outlive
Oil Rush
APOX
World in conflict
RUSE
Wargame EE
Glest
Globulation 1/2
Battle Realms
Halo RTS(Can't care much for a console only RTS, but I'd like to give it a go anyway)
Mobile games:
Z Origins(android)
Rusted Warfare
Upcoming:
Planetary Annihilation
Command and Conquer(previously Generals 2)
Sucky games(I didn?t like these games):
Battle For Middle Earth II(plays like a bad mod of the first game)
Rize of nations: Rise of legends(was pretty bad)
Companey of Heroes(Great single player, sucky multiplayer, Lots of other people swear by this game, so try it out anyway)
Universe at war: Earth assult(some cool ideas, such as the faction that uses crawler bases, but has some pretty bad gameplay and a terrible single player campaign)
Star wars Galactic battlegrounds(star wars reskin of Aoe2, pretty cool if you're a star wars fan, but the gameplay is out and out worse than normal Aoe2)
SunAge(australian made RTS game, has some cool ideas, but their attempt to make unique gameplay ruined the things that they got right)