I have pretty similar tastes to yours in gaming, I think. I seem to remember us even having a discussion about the merits of X-COM: UFO Defense in the shoutbox. Back when there was a shoutbox.
Civ is a good series, but is more of a higher strategic level than tactical. Kind of like X-COM, but more involved and without the turn based battles. So not really like X-COM at all, but you get the point.
I seem to remember enjoying
Fallen Haven as a lad, but the rose-coloured nostalgia glasses might be coming into play on that one. It's not actually out of the 90's, and good luck actually finding it, but it is more recent than the other games you've mentioned, at least.
The turn-based strategy game is a lost art form.
Wesnoth is one that I've enjoyed, with the added bonus that it's available to a Linux nerd like me. One of the things that I like about it is the balance. Each faction plays differently and requires different strategies to use effectively, but no matter what side you're playing, if you expect your level 3 unit to wade mercilessly through swarms of level 1 enemies you'll be doomed to disappointment.
And staying in the 90's, the Master of Orion series is also excellent and has not been mentioned. Master of Orion 3 was a bit too hands-off for my liking, but Master of Orion 2 was widely acclaimed, and with very good reason. All the fun of building a galactic empire, combined with large scale turn-based space battles. What more could a guy want?