Gen I - Pikachu, pokemon mascot highly marketed of course. Pokemon of Ash and Red both main characters of pokemon anime and manga respectively. The mascot of Pokemon Yellow. It was also featured in SSB and Melee along with Mewtwo(Melee only) who I think is highly popular as well.
Gen II - I really don't know about this generation, to meet it's between Togepi because it was on of Misty pokemon, Ampharos since me and my friends always like it. Or Larvitar family, I always fancied this family.
Gen III - Again many pokemon that I can think of. SkittyXWailord.
Blaziken was features as early as the Silver conference by Harrison and demonstrated how powerful it was. Milotic I always thought was popular, it seemed like a Pokemon made for contests due to how it first evolution was evolved by Max Beauty. It was also featured by Wallace 8th Gym Leader in R/S and Champion in E. The Pseudo Legendaries Salamence and Metagross where also popular being featured by Elite Four Drake and Champion Steven respectively.
Gen IV - Lucario hands down. I don't know how many users on various forums I have seen with Lucario as their user name, that indicates it's popularity alone. Not just that but it was also featured in 8th Movie Lucario and the Mystery of Mew. And to add to that is a prominent pokemon on Gym Leader Maylene and Champion Cynthia Teams. On top of this it was featured in SSB Brawl.
Gen V - Since this is a new generation I can't exactly tell. I know a lot of people like Snivy which they still call Smugleaf. Zoroark just because of the fact that it was the first 5th Generation pokemon introduced, and it was featured in the 13th Movie Zoroark: Master of Illusions which even bears it's name. Also the ever fan favorite N has Zoroark as a prominent member of his final team. I have seen a lot of people support Shandera avys and sigs on various forums so this may indicate a slight following for this pokemon. Kibago family, one reason being it is Iris signature pokemon another being it's high attack power and that it is a Dragon pokemon of course. Like Shandera I find that I see many people have either Kirikizan in their avy or signature indicated a following for this pokemon. Wargle as I previously mentioned I have seen this featured in quite a bit of signatures. Also part if Cynthia BW team. Sazandora being a pseudo legendary it seems some what popular. Ulgamoth it is featured my Champion Adeku and again I have seen this in multiple peoples signatures thus indicating there is some sort of following with this pokemon.
