Mostly just making a compiled list of what's already been said but might get some new ones as well.
There's the MGS HD/Legacy Collection (preferably get the HD collection since you already have 4) and MGS5 Ground Zeroes.
Deus Ex Human Revolution.
Splinter Cell HD Trilogy (has the first three games) Double Agent (though if you have a PS2 get that version) Conviction (if you have a 360 or game on PC) and Blacklist.
The Hitman HD collection, Absolution also has decent stealth gameplay.
Also, while they're not 100% stealth games, Elder Scrolls Oblivion, Skyrim and Fallout 3 and New Vegas can be played sneaky like.
The Tomb Raider reboot can also be played with stealth.
Again, not a complete stealth game but Walking Dead Survival Instinct has pretty OK human vs zombie/walker stealth.
Batman Arkham Asylum and Arkham City has decent stealth gameplay, haven't played Origins so I don't know about that.
Again if you have a PS2, there's SOCOM US Navy SEALs 1, 2 and 3, if you've got a PSP there's Fireteam Bravo 1 2 and 3.
If you have a 360 or game on PC there's Velvet Assassin.
I'd add the Tenchu series (from the makers of Dark Souls). They sort of fell out of style, but I was never sure why as the gameplay was exceptional in all of them and the last, Tenchu Z, was fantastic.
This would be reaching, but there's a multiplayer co-op shooter called Payday 2 in which 2/3 of the scenarios are designed so as to be possible to be stealthed, though not easily.
Otherwise, this is pretty comprehensive for consoles.
Deus Ex: Human Revolution, the two most recent Splinter Cell games, and Alpha Protocol, if you can stomach some unpolish. All of those games use cover-based stealth (the newest among my favorite genres), and they also have RPG elements that allow you to customize your play style and abilities.
Watch Dogs has stealth sections, too, but there's also a lot of driving. I'd recommend that, too, though it has less stealth than the ones I just discussed.
"No matter what, you keep finding something to fight for." -- Joel, The Last of Us