Great thread idea!
10: Captain Falcon - An amazing man, and just all around good character. Know him mostly through memes and smash of course. If I had tried out Fzero GX (I believe he appears in it (?) ) he might have earned himself a higher ranking.
9: Tom Nook - The only realtor to hold a candle to Phil Dunphy. Also the best thief in gaming.
8: Wuhu Island - This might be cheating, but I remember seeing Miyamoto calling it a character, because they tried to make it something that you would get to know and relate to, much like mario. I played a ton of wii sports resort back in the day, and also a bit of wii fit plus. I still remember quite a few of the islands landmarks, so I probably know more about this "character" than any of the others on the list.
7: Marcus (?) - The rival from pokemon diamond, the game that made me a gamer in the first place. He might not be all that hard to beat, but is nevertheless a character I have fond memories from besting.
6: Ike - My main in smash, and nothing more than that really. :P
5: Tharja - Some really fun dialog with her in awakening, just all around great character! Pretty as well!
4: Link - It might be mostly because the games are godly, but I do think Link in many ways are the perfect hero.
3: Luigi - Having enjoyed a few Mario and Luigi RPGs have made me realize that Luigi is the most amazing sissy out there. Simply a lot more fun and interesting than his brother.
2: SA-X - Maybe somewhat untraditional, but fusion was my first metroid game and SA-X certainly made that game for me. No enemy has gotten me actually frightened in the same way this beast has.
1: Melia - What a complex character she was. Fantastic in battle, and by far the most interesting character of the game IMO. Try out Xenoblade if you already haven't, you won't regret it!