Other 'top X games' votes I've seen appear to deal with the sequels issue on a game-by-game basis, depending on how different the games are. So a vote for, say, Doom 1 would be counted with the votes for Doom 2 as they're very similar games. However, a vote for GTA (the original) wouldn't count the same as GTA 4 as you wouldn't even recognise them as being related.
Unfortunately that only really works if you're all in a room together deciding, so I vote it's done on a game-by-game basis. Might not be fair to GTAs, but doing on a franchise basis gives rise to problems with games like Half-Life 2 and Portal (they're utterly different, but share story elements) , or Crysis and Far Cry 2 (both essentially sequels to the same game, if very different). Plus, with franchises there's usually one that stands out that would be voted for anyway.
Edit - nice to see this back btw