RTS is pretty broad so it's difficult to pick a favorite. If we narrow it down a bit though:
Going for the more traditional style of rts, with trivial resource gathering and basebuilding:
KKND Dark Reign Both are great fun, but quite difficult, especially the latter.
Straying a bit from the more traditional feel by adding some nontrivial base management, there is the excellent
Stronghold Starying further away still from the traditional rts formula, there is the timeless and utterly fantastic
Populous Going the tactics route, with all base building elements removed there is the 'realistic'
World in Conflict and the futuristic
Ground Control and
Ground Control 2 Finally, if you can't go wrong with [url=https://en.wikipedia.org/wiki/Command_%26_Conquer:_Tiberian_Sun]Tiberian Sun[/url] which has been free since 2010.
Another game you could consider is
Battlezone which, although played from first person perspective, has rts base building elements (placing refineries, turrets etc.)