The original Tenchu was awesome, but that's a Playstation game, so... The first three or four Splinter Cell games were fairly heavy on the stealth aspect too, until they kind of dropped it on its head in Conviction. Stealth Bastard Deluxe also seems interesting, but I haven't personally played it yet.
Deux Ex/Deus Ex: Human Revolution have elements of stealth, as does the Batman: Arkham series, but they're a bit more focused on action than most.
Overall I'd say the best pure stealth game out on Steam right now is probably Mark of the Ninja. It's absolutely, jawdroppingly amazing.