If you go purely by sales, its Pokemon, Mario and Zelda. But if you're going to go into things like 'popularity' and 'Quality', the context gets highly skewed.
The reason Metroid is often put as #3 in the list of Nintendo's 'core titles' is because it was stated by many of the heads of Nintendo to be as such. A 'third pillar' of Nintendo's main three gaming series. If you also go back and look at the origins of the NES, its very creation was to be a game to succeed Mario and Zelda, in both scope and originality.
Any way you slice it, obviously Nintendo has series that do better sales wise (and are more popular). But the reason why Metroid is counted as the 'other other' main title in the Nintendo line-up is probably simply because, like it was designed to be, its the most similar in scope and design to a Zelda and Mario title. And deep down, people know when a new Metroid comes out, its going to be big. Even if only 1% of those who own the console play it.
Six upcoming games you should look into:
