Well, I guess it'd be a combination of sales (physical+digital), popularity in SK (Gallup, CF deals, song charting), international recognition (youtube views).
On that note, for the boy groups it'd be TVXQ #1 for early 2nd gen era and Big Bang for mid to late 2nd gen era.
For the girl groups, it'd be Wonder Girls #1 for early 2nd gen era and SNSD for mid to late 2nd gen era.