Civilization II - the best game I've ever played, period. I logged more hours in that game than most others combined I think. 

Steel Panthers......or......no....that's it....just Steel Panthers.  

EDIT:

Damn.....I had to edit.  I just cannot decide between the V for Victory series or Steel Panthers.  Well.......either way I loved em both equally so you pick one.......hehe

You are a man of taste.

I'd add Bandit Kings of Ancient China and King of Dragon Pass to the honorable mentions category. And Master of Mana, the successor to Fall From Heaven II, with far improved AI.

Well, the strategic part on the overmap is turn-based, if I recall correctly. So it does.

For me its a tie between Master of Magic and X-Com.

Then its GC(all of them)

Romance of the Three Kingdoms(many of them)

Gemfire(way old game from back in the day)

Civ series

FE

Age of  Wonders (1 & Shadow Magic) for me, I think. The magic part is cool and the races diverse. Also I really like fantasy settings. The combats where exciting too. The best turn based combat to be precise (for me).

I have tried MoM when it was abandonware, but I didn't like it. The races looked really shallow, and city building was a lame rip of from civillization. It's a shame, because the magic part looked more diverse than AoW: SM.

I also really liked playing Elemental: "Frogboy patch" (Part of the WoM series, it made the monsters insane!). I really liked the setting of WoM, survival against the harsh world (Insane monster settings), the wandering bands of monsters, returning the world back to life. Fallen enchantress was also nice, but I stopped playing after Beta 3 because I played the #@$% out of it during the Beta. Waiting for LH now and hoping that the wildlands organize raids now.

Alpha Centauri, of course. Beautiful, thematic lore built into a great game.

Xcom (original game, haven't tried the new one yet)

Master of Magic

Elemental Fallen Enchantress

Panzer General

Master of Orion 2

I suspect Legendary Heroes might even top MOM for me.   Nothing could top Xcom though.  What a fun experience! I still remember the first time I played it on my brother's computer.

Cheers,

Sword

It's kind of hard to pick just one as TBS by genre has had some real stand outs

Empire (Dos); All those Civ-Type games you came to love started from here

SSI D&D Gold Box series; I still love me some turn-based RPG

Original X-Com [Biggest influence on all TBS games released in the future]

Warlords; First fantasy army TBS I can recall

Master of Magic; Simply amazing, but so damn buggy, even after the patches

Final Fantasy Tactics; The most complex and satisfying TBS RPG I've ever played

Freedom Force; Customized Superheros, destructible environment, ragdoll physics, voice acting, and more!

Silent Storm; X-Com meets WWII.  I loved it.  Some of the scenarios are ridiculous hard

Personal Note:  I initially enjoyed the Civ game series, but found the end game to be so absurd contextually (Race to the stars before the planet is blown up or conquered) that no amount of mechanics, graphic updates, or skill tree expansions could make it fun to play. 

For its time, probably Civ II. But in terms of an overall gameplay experience, including immersion and feeling like I was really running an empire and competing/communicating with other real empires, GalCiv2 takes the cake easily. By far the most immersive, engrossing 4x game I've ever played to date.

Alpha Centauri is up there for its time, as well.

If you're gonna get flamed for it, so will I. Jagged Alliance 2 was an awesome game for its time imo.

Jagged Alliance 2?  Are you fucking kidding me?  That's the most...wait, I never played it, is it good?  I've thought about picking it up from GoG.com.