X-Com: Apocalypse
A very strange answer coming from me, I would say X-Com: UFO Defence, but then I remember how much more there is in Apocalypse. UFO Defence is very tight, nothing is wasted, every element is equally as important. But this isn't about which game is better, it's about which game is my favorite. Apocalypse is my favorite game because it takes every important quality from UFO Defence and takes it to incredible lengths. It gets higher appreciation from me over games like Deus Ex because when it comes down to it Deus Ex, while being one of the greatest games of all time, is still a fairly linear progression through a story.
Apocalypse is totally different each time I've played it. They gave it so many variables, the city has 27 factions, each one trying to accomplish their own goals, each time you start a new campaign the city is randomized changing the way those faction interact. At any time you can choose to attack those factions for whatever reason, you actually send a team to attack them, you go inside their buildings and take their stuff and kill their workers and security people, the faction is then forced to replace the equipment and personnel you destroyed, this affects their financial position in the city and their relations with other factions. It also affects how active they are, if you empty their operating budgets they can't be a visible force in the city.
Factions will enter conflicts with each other, and the private company that runs the police force and the government already starts out in conflict with the many criminal syndicates in the game. In one game very late, right before I was about to destroy the Aliens, The week ended and I was about to receive my standard X-Com Government subsidy and they increased my subsidy that week, but their income was so depleted from fighting in the streets with criminal syndicates that they were only able to pay me 5% of the normal amount, that was okay because I was making all my money through manufacturing alien technology at the time.
In one conflict a stray Justice missile from a Diablo gang's hovercar hit a building belonging to the Technocrats and leveled it, including all of the transportation conduit branching off of it, this caused the Technocrats to scramble their own hovercars and they totally destroyed Diablo's hovercars and one of the slums owned by Diablo. The Extropians hate the Technocrats because they are political rivals, so the Extropians allied with Diablo, when the Technocrats destroyed Diablo's slums, one of Diablo's gang rivals, Pyske, allied with the Technocrats, and from that point on, each gang was effectively being supported by these two political lobbyist groups. Then when the Aliens managed to infiltrate and control the Extropians and I began raiding them, I found myself in higher standing with Pyske and the Technocrats.
Apocalypse manages to pull off complex political intrigue, if you took out the aliens and added a slightly more complex market it would still be a great game about a city in the future where corporations have their own armies.
And, you can go to a corporations facility with 25 people armed with 2 disrupter cannons each and literally level the building piece by piece, completely vaporize the supports and let gravity bring everything above it down, including their people who will be crushed under the rumble.
Long story short: You can vaporize an entire sports stadium with hand held weapons in real-time for the purpose of bankrupting the league...oh, and there are aliens.