Have I played all of the stealth games?!!!!!!!!!!

"Excluding games I haven't played from the above franchises"

Manhunt
No One Lives Forever
Sly Cooper(if you have PS)

Fallout 3, New Vegas and TESV: Skyrim and IV

Death to Spies, Elder Scrolls, Commandos are the games that come to my mind. Elder Scrolls is a Stealth game if you want to, but i recommend you Commandos especially.

Far Cry original is the only Far Cry game with decent stealth.

Sniper Elite v2

Commandos, Desperados (specially the first one), Tenchu, and i think Syphon Filter can be played with a stealthy focus.
Oh, and DO play the first and second thief whenever you can.

Play the first three Thief titles. If you can't stand older graphics, there are graphics patches for these games. But I like them better with older graphics :D It is likely that you will have some issues running these games on newer hardware, so make sure you install patches for these three games first. You can contact me for this if you like, or make a simple search about TFix, TafferPatcher and Sneaky Upgrade.

Also, you can try The Dark Mod (a Thief-like game formerly a mod for Doom 3, now a standalone game after the id Tech 4 was made open source), which is completely free. You can download fan missions for this one in-game or from some websites.

Edit: Your footnote slipped my notice, but anyway you can still play them if you haven't, or I strongly recommend you The Dark Mod.

If you can classify Just Cause 2 as stealth, you can justify calling pretty much any other game stealth.

There's nothing stealthy about kamikaze bombing an enemy base all guns blazing then jumping out at the last second on a parachute.

No One Lives Forever 1 & 2
Prisoner of War
Sniper Elite
Commandos: Strike Force (unlike the others, FPS)
The Saboteur
History Civil War: Secret Missions
Warp

Beyond Good and Evil.
It has amazing story, and there are kinda difficult stealth parts. It's an old game but it's awesome really, try it.

Watch dogs is going to be stealth

Both Payday games have some stealth in them. Also like someone said, Fallout could be (along with Skyrim) depending on how you want to play. I believe that games such as Amnesia require some stealth to stay alive but that's different than most stealth games. Hidden Source Beta, multiplayer, and stealthy a bit if playing as The Hidden. Also someone mentioned Velvet Assassin, I haven't player it but the reviews are bad, especially around the stealth mechanics.

Thief 1 2 3 (check ttlg.com for TONS of custom missions)

Alpha protocol. And the splinter cell franchise

Path of Shadows!

Payday 2

Thief The Dark Project
Thief Metal Age
Thief Deadly Shadows
Chronicles of Riddick - Assault on Dark Atena and Butcher's Bay

Commandos: Behind Enemy Lines

From back in the day when games didn't hold your hand and walk you through it.

Rogue Trooper - even though at 1st glance it may look like gun and run most of sections will have to be passed by stealth using your sniper with silincer attached + the game itself requires precise shooting. Sadly the game is short(but can't remember how short exactly)

Rust and DayZ, haven't played, but you could simply be stealthy and kill people, loot towns etc.