Ever since the beginning Cubone was my favorite. Maybe I'm weird, but I think it's cute. Then when it evolves, all that cuteness becomes coolness. I'm not keen on some prop Pokemon (Farfetch'd, Conkeldurr), but I think it really works with these two.
Also,
Fennekin
The one who took Squirtle's place as my favorite starter after all these years. Isn't that the most adorable thing you've ever seen? Plus it evolves into an awesome fire mage.
9) Skitty
Cards.
8) Meowth
For whatever reason, I just love collecting meowth cards, but I never really use him much in the games.
7) Ampharos
Cards!
6) Flaaffy
CARDS!
5) Mareep
Yet another collection of cards
4) Slowpoke
I think this is probably a unpopular opinion, but playing Heartgold and walking around with a Slowpoke behind me made me fall in love with the little dope.
3) Pikachu/Dundabolt
I have collected tons of pikachu cards. Call it a hobby.
2) Lucario/Akey
Beating Korrina when you battle Lucarios, I actually beat her and I asked my friend what I should name my newly acquired Lucario, she said Akey, and the name stuck.
1) Infernape/Chimmy
At number one we have, of course, my very first pokemon ever, Infernape. Aside from Chimmy being the worst nickname for a starting Chimchar, he has really stuck with me for ever. I have an interesting story surrounding this pokemon, when black and white came out, I chose black as my game of choice, and I transferred my dear Chimmy to my black game, and then when I realized that I couldn't get him back from that game, I got very upset. Seeing me so distraught, my sister took my game, bred for a Chimchar, and then proceeded to trade with our friend who had cheated for lots of items 78 rare candies(because my Infernape's level was 79), and feed them all to him, and get my beloved Chimmy back.
My favorite pokemon ever of all time is dah dah dah daaaaaaaaaaaah shaymin only the best pokemon ever its a hedghog and a deer and shinly land shaymin is totally sonic.
There's something so wonderful about its wings, especially now that it actually has a good sprite in the sixth gen, showing the full beauty of its wings.
And there is a haunting kind of sorrow in the theme of Tin Tower/Bell Tower... Perhaps Ho-Oh longing for the inhabitant of the Brass Tower/Burnt Tower, Lugia, the other half of the balance?
It's also partially a nostalgia thing, as little as I like to admit it...