The original Deus Ex still has a great reputation for innovative gameplay as well as incorporating 'true' RPG elements into a FPS - not to mention having a great storyline and replayability.
The second had a number of issues, the most egregious being the 'universal ammo' - all weapons used the same ammo, just varying amounts per shot, meaning when you were out of ammo you were out for all the weapons. Much of it seemed to because they were trying to switch to console as the primary platform, making a less-than-satisfying PC experience, IMO.
The new one is my 'must have' list, right behind Fallout: New Vegas.