Thief is a fantastic stealth series, as... ah... almost everyone has noted above, and I'll always love the Tenchu games, Wrath of Heaven in particular (though I've not played the latest iteration).
If pressed though, I think my favourite would have to be Hitman. The idea of hiding in plain sight and planning your strategy before you attempt things is really unique, I think.
As for Metal Gear Solid... I'd say they might well be 'the best games that have stealth in them', but the actual stealth mechanics are some of the worst - they tend towards hide-n-seek rather than any sort of thinking or planning.