Updated: 9/25/2018
Game-RTS
0 AD (Upd: 2/21/2014)
RTS game like Age of Empires, but you can be one civilization from the year 0 AD: Greeks, Romans, Celts, Persians, Iberians, Carthaginians. [Report a dead link]
http://freecode.com/projects/0-ad

Bos Wars (Upd: 2/21/2014)
Like Command and Conquer. Linux only. http://www.oneonlinegames.com/download/bos-wars. [Report a dead link]
http://www.boswars.org/download.shtml

Colony free online RTS (Upd: 2/11/2014)
[Report a dead link]
http://armorgames.com/play/4264/colony

Command & Conquer JS (Upd: 8/28/2013)
This uses HTML5 and Javascript to play the game in your browser. Browser must support HTML5. [Report a dead link]
http://www.adityaravishankar.com/projects/games/command-and- conquer/

Command w/o Conquer (Upd: 4/26/2013)
Like Command & Conquer, but needs graphics from C&C: RA. [Report a dead link]
http://www.oneonlinegames.com/download/command-without- conquer-stef-alert

Enemy Nations (Upd: 8/1/2013)
RTS game, hi-res art, native network support. Appears to be multi-player only? But has some AI too. Complex economy.

Requirements: 486/66mhz with 64mb ram. [Report a dead link]
http://www.enemynations.com/features/index.html

Frontline Defense , 5,000kb (Upd: 10/15/2013)
Tower-defense game. [Report a dead link]
http://www.oneonlinegames.com/download/frontline-defense- first-assault

Glest (Upd: 10/15/2013)
Glest is a free 3D real-time strategy game, where you control the armies of two different factions: Tech, which is mainly composed of warriors and mechanical devices, and Magic, that prefers mages and summoned creatures in the battlefield.

Glest is not just a game, but also an engine to make strategy games, based on XML and a set of tools. A few mods already exist. [Report a dead link]
http://glest.org/en/downloads.php

List of free RTS games (Upd: 9/24/2013)
[Report a dead link]
http://www.oneonlinegames.com/download-games/rts-games

Megaglest (Upd: 10/15/2013)
MegaGlest is an entertaining free (freeware and free software) and open source cross-platform 3D real-time strategy (RTS) game, where you control the armies of one of seven different factions: Tech, Magic, Egyptians, Indians, Norsemen, Persian or Romans. The game is setup in one of 17 naturally looking settings, which -like the unit models- are crafted with great appreciation for detail. Additional game data can be downloaded from within the game at no cost.

Requirements: 1500mhz minimum, 1gb ram minimum. [Report a dead link]
http://megaglest.org/

Online Free RTS (Upd: 2/11/2014)
[Report a dead link]
http://www.games.com/real-time-strategy-games

OpenRA (Upd: 8/28/2013)
Like Command and Conquer Red Alert. [Report a dead link]
http://openra.res0l.net/

Widelands (Upd: 9/24/2013)
Widelands is an open source (GPLed) real-time strategy game. It is built upon the SDL and other open source libraries and is (and will always be) under heavy development. If you knew Settlers I & II (© Bluebyte), then you already have a rough idea what Widelands is all about because widelands is heavily inspired by those two games.

This is a really complex game. Be warned. [Report a dead link]
http://wl.widelands.org/