Meh, the story of Deus Ex is so poorly conveyed I can't be bothered with it. I've given my analysis of it previously, and care not to repeat myself on the subject.

Interestingly, Deus Ex actually manages to edge itself into my list of "clever games" by virtue of its design. The overall flexibility of gameplay (which includes story structure) is good enough to be thought-provoking by itself.

For me, the answer is Planescape: Torment.

Also, Ultima 4-7. Instead of giving you an evil adversary to kill (which was, and has become again, the rather bland default plot for RPGs), it presented you with a philosophy, encouraged you to learn how it worked (Ultima 4), warned about the dangers of enforcing well-meant ethics onto others against their will (Ultima 5), contemplated the importance of respecting and cooperating with different philosophies (Ultima 6), and warned about corrupted ethics (Ultima 7).

The best thing I can tell you two is to absolutely not read a single other thing about it and go play it.

Yeah, I figured that would be best.

Not a lot of these games around ... In my case, it's the usual suspects, I guess: Planescape Torment, Gemini Rue, To The Moon. Maybe also Trauma, to a much smaller extent.

I accidentally read a bit about Spec Ops sadly, but I still plan on getting it at some point. Just haven't been in the mood for something so grim.

Incidentally has anyone played
The Nameless Mod?
Richard from Saturday Crapshoot seems to think its pretty good:
http://www.pcgamer.com/2011/08/20/saturday-crapshoot-the-nameless-mod/
Once you get past the silliness and in-jokes, the fact that it actually lets you side with the bad guys sounds especially interesting...

Actually, as the crapshoot recently reminded me too, Suspended, the Infocom text adventure that I played on the C64 was pretty clever, you were in a guy in suspended animation who had been woken up to work out and solve whatever issue was about to make the nuclear facility he monitored blow up destroying the planet
You interacted with the world via 5 robots , each one possessing just one human sense but the seeing one 'Iris' (see what they did there?) is broken and getting her running again is one of the first puzzles
Never got very far with it but clever concept...