I don't think the last few Zelda games are as good as the older games of that series, just like the last few Mario games. They've really dumbed down some of the greatest game series just to make them more appealing to the mainstream.
The quality and greatness of Cave Story is nostalgia for the most part, but it also simply has great oldschool graphics and simple but at the same time deep and sometimes quite challenging gameplay. A lot of people may say that it looks terribly outdated, but they don't quite understand that the funny thing is that that really doesn't matter at all. At the same time it's quite a niche game though because of all that.
Same story, different game; Why is the game Soldat as popular as it is? Isn't it just 2d graphics and not so great looking effects? Wrong, it's perfect for what it gives experience-wise. Off course the gameplay itself is excellent too, a game that doesn't have good gameplay won't become popular very quickly.
Most of the games mentioned in this thread do a lot of things the 'good way'. I'm not talking about a 'x-factor' kind of thing here, a lot of these titles simply are very good games. I wouldn't ever have thought The Sims would become as popular as it is, but it's like someone said here before; the greatest games aren't always the most popular.
Lol, games like World of Warcraft are actually a disgrace to the gaming world.