Deus Ex is a classic, and is my favourite PC and PS2 game. It does have it's flaws, such as bad AI for the NPS, ugly graphics, some of the weapons/skills/abilities aren't as useful as they are when tweaked by a third party mod*, the story and setting doesn't always make much sense, the first level seems to be not as enjoyable as the levels that follow, and the game's quality does deteriorate towards the end of the game, but it's a mark of how good the game is that even with these flaws, you don't care since the game is so fantastic.
For a start, the story is mostly very good, and the levels (playing areas) are great. The freedom to use the objects and items you come across (be it a basketball, a pool table, or even just stack up boxes and dustbins to climb over a wall to avoid or shorten a dangerous situation is really good, and i's fun experimenting to see what the game allows) is great, and most situations have multiple ways to defeat them, from stealth to all out violence (the weapons you get can be really powerful) or often by using your brain. You can do almost anything you want, storywise, with the game being programmed to allow for you to deliberately complete or ignore most objective, to kill or save most characters, to basically do more or less what you like, though you must complete some objectives to continue the game.
The game is long, and has near endless replayability. It's almost a given that most PC Top-ten-Games lists have Deus Ex in them, because you can play it how you like, as a stealth game (it's in the Guiness Book of Records, seriously, as the first person shooter that needs the least number of kills to complete it - you must kill three people to complete the game, everyone else you can either kill/sneak past/knock out, or outwit, as you choose), or as a first person shooter with powerful weapons, or as a game where you can think your way past most situations, by using local items/machinary/hidden areas to avoid enemies.
It's just a very, very good game. It has lots of flaws, but still hasn't been approached, let alone beaten, at what it does since it was released fifteen years ago. It's first sequel, Invisible War, inexplicably did away with almost everything that made Deus Ex great, and it's much more recent sequel (well, prequel), Deus Ex: Human Revolution, was great but still not as good as the original.
* Third party mods like Shifter and GMDX alter the game mechanics, enemy AI, etc, but play the ordinary version of the game before you play it modded.