Homeworld II is a really good real-time strategy game. It is space-based, so your commanding fleets of ships (from little fighters and bombers to big battlecruisers). It also has a good plot, and I personally adore its music. It gives off a somewhat Dune-like vibe.
It may be a bit too combat-oriented though.
I am sure you know the next Total War is coming out. So that would be another one.
Old Skool (You'll need to do some leg work to get these to run on any modern day Win XP/Vista computer. But most of them are abandonware and thus free):
Advanced Civilization
Dune II
Populus
Lords of the Realm 2
Caeser II
Fantasy Empires (Bonus! This is a game based on the Mystara world!)
Castles
Castles II: Siege and Conquest
Transport Tycoon
A-Train
Masters of Orion (I believe the second one is considered the 'best')
Diggers
Colonization
Recent-ish:
Age of Empires II: The Age of Kings (much better than one, and IMO)
anything from the company Paradox
Galactic Civilizations 2 (with add ons)
The new Colonization by Firaxis
Civilization 4
Best part is...its totally free for download. Another great totally free game, and one of the best turn-based WWII strategy games of all time is Steel Panthers: World at War. Its a big download, but its really fun.