Hmm...
This would be easier if I focused on shooters as my principle source of enjoyment, but of the ones that I have played I'd put the Dues Ex series at the top, just above Portal.
The Dues Ex games [The first one, which I only played a demo of and the second one which I own] brought to me a sense of control few shooters have given me before. I actually played basketball in it. Something that may seem trivial to some people, but it just shows the level of interactivity within the game. You could interact with just about any object that wasn't bolted down to the ground, you could turn things on and off, and all with the addition of being able to blow someone's face apart and a genuinely interesting storyline.
Portal was a quirky, short, puzzle game in shooter format which I adored immensely. One of the few faults with it, though, was the lack of violence. Now some people may see that as an odd statement, but when I play shooters I expect to do just that -- Shoot things. I don't really play them for storyline, or for puzzles, or for quirkiness -- I play them to blow shit up, and shoot people in the face. While Portal was very enjoyable, and I have replayed it a few times, it just didn't have that stress relief of blowing things up that I look for in shooting games.