I replayed Vagrant Story on an emulator three years ago and it still holds up as one of the greatest games of all time, in my opinion.

Me too. I'd buy it immediately.

Not really favorite, as I pretty much never game on anything but PC, so more of a "console-only games I'd like to play" list.

I'd say the middle of the Mortal Kombat games (Deadly Alliance, Deception, Shaolin Monks and Armageddon). Would be nice to have official ports instead of having to emulate.

Out of curiosity, I'd also probably give Drakan 2 (Drakan: The Ancients' Gates) a go. From what I've seen/read of it, it's much worse than the original (extremely console-ified), but still would like to try it myself.

Most any of the Zelda games, but if forced to pick one it would be Majora's Mask

Metal Gear Solid 3 or Xenogears.

Grand Theft Auto Chinatown Wars: I spent an insane amount of time on this game, especially on the NDS, and on PSP for multiplayer matches.
I don't know why the game is so unknown to the public, but I think that the NDS metacritic rankings may change that

I don't think it will ruin the nostalgia, seeing as you have the option of using the original graphic and music (and can change them any time), and it even copies much of the original game mechanics, including one particular glitch and the behavior of the RNG (to the point where RNG manipulation is still possible).

I do, however, one warning about flashing lights: When using the original graphics, whenever you damage a boss, the screen will flash red. If that is a potential issue (for example, if flashes give you epileptic seizures or are even just somewhat unpleasant), you can avoid this by switching to modern graphics whenever you're fighting a boss.

Just want to add that graphics and music can be instantly changed, in real time, by a simple button press.

Oh, and it runs full speed in any computer made in the last 5 centuries.

You're welcome.

I believe that warnings like this are very important, so that players can judge for themselves whether they can safely play the game, and can choose to avoid the game *before* the problem arises, or change a setting or find some other way to avoid the flashing lights if it could be a problem. Since you're not affected, it is (likely) safe for you to ignore the warning, but for players who are negatively impacted by flashing lights, they can know ahead of time.

It also helps that the game does have a nice work-around, as I mentioned; just switch to modern graphics whenever you encounter a boss. You don't even need to go into the menu to do this! (As Dark_art said, a single button press will change the graphics.)

I've actually seen a speedrunner switch to classic graphics before each boss fight to avoid the short cutscene that shows the name of the boss, and then switch back to modern once the fight starts in order to avoid the flashes, so that the stream would be safe to watch for those affected.

Oh, definitely very important information. As no one knows (in advance) whether something of significance in a game may affect someone else personally or in how they approach or play the game, or possibility that it could even be potentially dangerous.

N64 Goldeneye

Parasite Eve and some other exclusives, like Metroid Prime.