I agree with the people above who recommended Alpha Centauri. If you liked Civilisation there a good chance you'll like Alpha Centauri. Personally, I liked it so much that now I can't pay Civilisation games anymore. The moment I see their factions and the "differences" between them it makes me cry.

- Heroes of Might and magic series
- Kohan Immortal Soverign : Very good old fashioned RTS pretty innovative for its time.
- The guild, of course
- Alpha Centauri


Those that aren't on GOG (yet ?)
- Europa Universalis series (Don't let those nay sayers about how complex it is frighten you)
- Crusader Kings II (same recommendation as EU)

I agree. After having played Alpha Centauri I have a hard time enjoying the Civilization games. I keep comparing them and Sid Meiers Alpha Centauri, SMAC, always wins.

The Europa Universalis games is a case of when you have learned the basics you can decide yourself how complex you want it to be. They're perfectly playable without fiddling with everything.

The first two Kohan games, Kohan 2 is actually the third game, Kohan: Ahriman's Gift is a Standalone "expansion" for Kohan: Immortal Sovereigns, are still innovative. No other RTS I know of plays like them.
Which is both good and bad. Kohan: Ahriman's Gift is my favourite game and I dare say that it's brilliant. But I might be a bit biased. ;) Wonderfull games.
The bad thing is that there aren't any other games like them.
So if you like RTS and would like to try a novel take on the genre I recommend the Kohan games. Beware though that Kohan 2 play markedly different from the first two.

Edit: Timegate Studios did one other game with the Kohan engine that is also very fun. Axis & Allies. Published by Atari I think. The setting is World War 2.

Since you seem to be after realtime strategy too, no collection is complete without total annihilation (and only the first one)

Lords of Midnight.

Already been mentioned a few times but you really can't go wrong with Alpha Centauri if you like Civ.

Dungeon Keeper 1&2
Total Annihilation
Earth 2150
Roller Coaster Tycoon series
Tropico 4 (5 is on the horizon)
Total War series
Supreme Commander
Sim City 4 Deluxe

Some awesome recommendations in this thread. You can't go wrong picking one or picking all :).
Some of my favorites here on GOG are SMAC, Colononization, Master of Magic, Master of Orion 1/2, Eador.
Don't have all these yet myself but have spent countless hours playing them in the past. Working to getting them here along with about 100 other games I've never played but are highly recommended.
Good luck and happy gaming!

If it's a GOG game you're after, Sim City 2000 might fit your bill. I always preferred SC3K, but for the price SC2K is a nice addition to your catalogue.

WOW. So many helpful replies.
I'm going to check out all of these recommendations now.

Thanks again everyone!