Please post a video that shows off the gameplay mechanics you're talking about, so that I can more easily add it to the list.
- Splinter Cell: Chaos Theory
- Hitman 2
- Assassin's Creed
- Thief
- Metal Gear 2: Solid Snake
- Oddworld Series
- Beyond Good and Evil
- Dark Messiah of Might and Magic
- Tenchu series
- Spiderman 1
- Alien vs Predator 2
- Riddick Series
- Batman: Arkham Asylum
- Sheep Dog n' Wolf
- The Saboteur
Here's another interesting video I found, called "a tribute to Stealth Games".
I've played all the Splinter Cell games released so far and there's no doubt in my mind that Chaos Theory was the best, both for the singleplayer multiplayer (which had the co-op removed and got super dumbed-down for Double Agent - even if it was pretty imbalanced in Chaos Theory). The AI was great, it was especially fun to screw around with them, and listen to them get more and more freaked out. They'd also notice broken doors, as well as (obviously) dead bodies.
The only issue would be the Starforce CD protection that installs itself without asking for permission. Oh, and the music (by Amon Tobin) was just awesome!
edit: here we go - favourite track
Hitman 2 is the only game of that series that I've tried out, but I had loads of fun playing it - unlike Splinter Cell you get to choose to a greater or lesser degree how you carry out the mission (though there's often one way that's sort of implied).
Hitman offered disguises which were always fun, and while the AI was exceedingly fickle it made things a little more interesting that just staying in the shadow till the enemy went past you.
Ultimately I haven't played that many stealth game aside from the Splinter Cell series, which is why I need help from you guys - played any game which offer an interesting new take on stealth? Failing that, do you know of any games that do the whole "hiding in the shadows" thing particularily well?