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.