Dark Reign (1997)

Auran's Dark Reign sat somewhere between StarCraft and Total Annihilation and was part of the huge flood of RTS titles that appeared in 1997. Its a 2D strategy game but with many of the advanced command systems used in TA, as well as many interesting features that took it well beyond the usual guns and armour thing. Terrain and some nifty commands could change unit movement and behaviour of units dramatically.

Dark Reign 2 (2000)
The sequel is a true 3D strategy title by a completely different developer, Pandemic. Pandemic also produced Battlezone II, a blend of first person action/strategy where you control a small squadron of armed vehicles.

Ground Control series (2000)

A futuristic 3D tactical title from Sweden's Massive Entertainment, emphasizing tactical action without any "tedious" economic stuff. Two forces, a large corporate entity known as the Crayven Corporation battles the fanatical religious Order of the New Dawn for possession of a distant planet containing a secret. Fast, furious squad level that has a unique (to RTS) net gaming feature: net gamers can drop into a Ground Control netgame at any time, deathmatch style. While aging a little bit these days, it still barrels along at high speed.

Expansion: Dark Conspiracy (2001)

Ground Control II: Operation Exodus (2004)
A well received sequel that built on the original, featuring (then) cutting edge graphics.

KKND (1997)

Krush, Kill 'N' Destroy, by Australian developer Beam Software, is a basic sort of game that came with the deluge of RTS's when the genre was "discovered" in 1997. Its your standard, post-apocalyptic end game: survivors versus mutants, but with a sillier tone.

Expansion: KKND: Extreme (1997)

KKND2: Krossfire (1998)
A superior sequel. Technically competent, highly derivative and I suspect you'll either get the Mad Max flavoured Aussie humour or it'll fall flat on its face in front of you. To give you some idea of what I mean, I have it on good authority that the title of KKND2 was originally going to be Caravan of Carnage. Alas, bad Ewok jokes would probably have just led to legal trouble back then. KKND2 was Beam Software's brief moment in the sun - I'm not really sure what ever became of them. Why, there's even some rabid fans petitioning for a KKND3, , and lamenting the quiet desolation as the last version slips away to the lands of abandonware...

Shattered Union (2005)

Warzone 2100 (1999)

One of th every first strategy titles to be fully rendered in 3D, Eidos Game's Warzone 2100 has all the usual economic, research and strategy elements with a few extras tossed in. You can design your own units from researchable components to produce hundreds of different unit variations.The only problem with all this is that your units still look like tiny little painted matchboxes on a small tabletop. Warzone's original developer, Pumpkin Studios, has gone bust, and the fan base has huddled the tanks in a circle in an effort to keep the game alive.

Since then, after many owners, trials, and tribulations, a fan group known as Pumpkin-2 managed to successfully petition the publishers for the game's original source code and make Warzone 2100 part of the Open Source movement. They've since produced a new patch, a multiplayer server and a website to go with it. You can peruse its forums here.