These kind of voting isn't influenced by regional factor (unless only japanese gamers would be accepted to vote).It would be nice to haven even more detailed which differentiates between NA and EU. I guess it would be more even on the EU side.
Nor by the original console sales because both Mega Drive and SNES were more or less equal outside Japan.the genesis came close to snes numbers (40m to 49m in some reports, but others peg the genesis somewhere at 29-33m as well), and the game gear occasionally outsold the game boy in america. i think nintendo's handheld line guaranteed a way for snes era games to get into peoples' hands into the later game boy, gba, and ds era, and the virtual console allows for a lot of that opportunity as well. sega could never get that same level of visibility in later generations.
SNES vs Mega Drive (Genesis)



http://www.neogaf.com/forum/showthread.php?t=1059657
What influence greatly these kind of voting are
1) Strength of the legacy software: Nintendo is the company that more proactively promote their legacy software as the best and more iconic therefore their legacy games have better exposition than others.
Since many gamers experience these games after the generation ended (even those that had a console during the generation because they were unlikely to own many games) there is a tendency to favour Nintendo.
2) Consolidation of the legacy software: By now it's evident that there is the emerging of a consensus of what is the best (see the many retrogaming top 10 available on youtube, many of which extremely predicable) which means a restrict number of games have precedence over the rest in a top 10 chart because there are so few spots that voters tend to choose "safe" choices.
Consider Chrono Trigger.
The game didn't sold that many units outside Japan and even the re-release on DS didn't sold that well but its iconic status as one of the best JRPG ever is so strong that it was easy to predict that it would finish in the first few spots in the final chart.
This is another good example.
If it was a question of just what sold best at the time of release, PlayStation software catalogue would have dominated however this isn't what happened because what really these votings highlight is the consensus on what is considered the very best which tend to favour a very small set of iconic games.