Note that these are not necessarily the games I strictly find the best overall, but rather those I found best for my own taste and preference. Surprisingly or not, I still do play all of these, at least occasionally.
Elite 2: Frontier
I had played the original Elite, but it was the sequel that kept me at my humble old 486 for endless hours. The sheer size of the procedurally generated universe, along with the complex trade, mission system, traffic and ranking, made it incredibly attractive to me. There is always something to do in the world of Frontier, and even when everything's fine, there are always new ships to try and systems to explore. There is a subtle hypnotic quality about this game once the player progresses into the heavyweight class.
Mortal Kombat 1
Though I have never been too much of a fighting games fan, this one is an important exception. I play (and like) other sequels as well, but the first one has a quality no other fighting game ever had in that amount: balance and tactics. This is truly a fighting game where one can win by just wisely choosing counterattacks that usually cannot be defended. It is therefore excellent and highly playable both in singleplayer campaign and in 2-player game. It was revolutionary for other reasons too, but these excellent fighting mechanics, which become apparent only once the player really gets the hang of the game, remain the absolute top.
Elder Scrolls 4: Oblivion
Before and after Oblivion I have played also the other Elder Scrolls games, and while Skyrim comes close, it was Oblivion that probably made my longest uninterrupted gaming stretch of all time, counting hundreds of hours until I played through all quests, all challenges and explored nearly all items. The amount of free roaming available here is incredible, and the views are insane. Still nowadays I like to load some random savegame and play a random quest.
Ahh, the godfather of all the space sim games, and one of the two Star Wars titles to enter this list. Every several years I tend to play this one from start to finish, and each time I enjoy it just the same as in the late 90's. It has everything: a great story, fantastic mechanics, atmosphere, and the rare opportunity to play as the bad guy. Not that I have much against rebels, but this game was simply better than the X-Wing. I prefer the original version to the CD, due to its adaptive music.
While on the topic of Star Wars, the FPS I never had enough of, and still do not, is Dark Forces, both the original campaign and many custom missions made by the community (with even my humble addition). By today's standards it is of course antique, but the mechanics and the level design make it very enjoyable. The Star Wars atmosphere is really depicted well here, the weapons and the enemies force the player to think cleverly, and there is something to actually do in the missions, not just kill all and reach the end switch.
Tomb Raider II
I've played all the Tomb Raider games, but searching for the Dagger of Xian remains the peak for me, for two reasons: fantastic playability (which actually deteriorated in several sequels) and a textbook example of super-grandmaster level design, fitting well into the story. It was slightly better in that respect than the TR3, though the call is close. Still I often start the game and find myself devoting hours to it, typically in the underwater or the monsatery levels - but I admit all are brilliant.
The one FPS I must have logged the most hours with, and mostly because still now I keep finding new ways of solving the missions and the levels, discovering paths and secrets. What I especially like about this game is its ability to subtly adapt to the players game style: stealthy, all guns blazing, methodical flanker, or something else. Even with the cringeworthy story and a few Hollywood cliches, this is still something to enjoy a lot on rainy afternoons.
It's hard to have enough exploring, building, constructing machines and repeating in this game. Originally I had bought it for curiosity, not expecting to play it for more than a few weeks, yet it caused a minor mania for me. I'm no longer surprised this game has so many players. And the projects that the fans often develop and present are incredible. Similar to Frontier, there is always something interesting to do in this game, even once you've gained all the achievements.
F-117A Night Hawk
From time to time I play aircraft simulations, but for the people that prefer methodical, calm approach to flying, this is the game to play (and I haven't yet found any other modern equivalent!). Namely, playing as the pilot of a stealth aeroplane makes it much more tactical, with long stretches of quiet cruising, just to fire a missile and return home, hoping to have been unobserved. The game is not trivial, and again not overburdened with detail as many other sims tend to be.
Indiana Jones and the Fate of Atlantis
Of all the point-and-click adventures, I've got to point this one out, yet Monkey Island 1 and 2 come close. This one is at the top because it has it all: multiple paths (some random-chosen for the player and some freely choosable), gorgeous graphics, interesting and sometimes hard but always logical puzzles, atmospheric music, a well-developed plot, and a good technical execution. Even though the replay value is not too high, I find myself playing this game time and time again.
X-Com: Terror from the Deep
Do I have something about the second sequels or what? But this one is indeed better than both the original X-Com and the latter X-Com games. It improved upon the successful formula of the predecessor, but did not overdo it. Very atmospheric, interesting and with lots of replay value due to procedurally generated missions and many possible approaches to stop the alien invasion. Usually I prefer the updated later version with some bugfixes. And the music is perfectly creepy (btw: I talked to the composer of the game, excellent guy).
The only N64 game in this lot, this is simply a game that feels so good to play, and refined to the last pixel, it keeps being enjoyable. Many possible approaches to solving the mission, great storyline and level design, well balanced gameplay and cool weapons make it one of my all-time favorites. A game that allows the players to play using their own style. Comparable to Perfect Dark, but I find GoldenEye just that bit cooler.