I think MGS is a pretty good example of how not to do stealth. In MGS4 there was absolutely no reason to do it, despite the fact that, of that series, it worked the best, since it was easier to just kill everything and there is no real reward or reason to not do just that other than to get a questionable title-thingy. In MGS1, the stealth was a lot more necessary, but the game felt like one big boring version of Pac-Man. You moved from location to location while the "ghosts" followed very pre-determined paths.
For modern games, I think Arkham Asylum has gotten it the closest to feeling "right." Since being seen results in you being shot to death in a lot of situations and you can approach most situations from any number of stealthy perspectives. You really need to balance freedom and speed of movement with stealth and action. There's nothing more lame that crawling for 10 minutes to move 20 feet.
For modern games, I think Arkham Asylum has gotten it the closest to feeling "right." Since being seen results in you being shot to death in a lot of situations and you can approach most situations from any number of stealthy perspectives. You really need to balance freedom and speed of movement with stealth and action. There's nothing more lame that crawling for 10 minutes to move 20 feet.