A few. My Japanese Manaphy from the wi-fi event. I ended up trading it for a celebi, which now I really regret. Then, my Japanese dittos, because I had no idea how valuable they were for helping other people fine shinies.
Even though there's nothing special about my pokemon in my team which are helping my defeat the Johto story, I'm still proud to own them. My Ampharos (Yang), Geodude (Toph), Togetic, Growlithe (Naito), Espeon (Aria) and Phione. I think you just don't forget those pokemon. I used to train only my starter until I defeated the game, or a couple other pokemon to help me win the leagues, I now train my whole party. So it's a different feeling.
I know it sounds corny, but I'm proud to have all the pokemon I use. Whether they're rare as Dragonite or common as Rattata, I like them all and would not change any of them for the world.......apart from my Graveller I used in Diamond
That said however, I would like to make a special mention to my Blaziken, without whom I would never have completed my very first pokemon journey or played pokemon as a fan.
For me its my Pokemon I got from the Pokemon Ranger Almia game. I was terible and that game and it took me forever to finish it so I deeply treasure my Darkrai and Riolu(now Lucario) because I had to work so hard to get them. The Manaphy was great too but you get him early on without having to beat the game the way you do with the other two
Two days into my first-ever attempt at IV breeding, I finally managed to hatch a Jolly Mienfoo with Regenerator and flawless Attack and Speed about half an hour ago. It would have taken far less time if Gallade was in the damn Humanshape group like it should be (ironically, Mienfoo looks nothing like a human ). I got a shiny Gallade with flawless Attack and Speed and awesome as that is, I wanted my Black team to only have Unova Pokémon so I decided to go with Mienshao. When I went through my boxes looking for Ground or Humanshape group Pokémon with flawless Attack or Speed, I came across that Gallade, and I couldn't help but feel like it was secretly mocking me.
"I'm Gallade. I have flawless Attack and Speed and I'm vaguely human-shaped. What's that? You want to breed a Humanshape group Pokémon with flawless Attack and Speed? Well too bad, I'm indeterminate because fuck you, that's why."
So yeah, considering the effort I had to go through to get it, I'm pretty damn proud of the little guy. Too bad it's not shiny. I think I'd die of happiness if that happened.