I'd have to say my Meganium on my old Pokemon Crystal file
I literally thought he was just my coolest 'friend' ever back when I was playing that game and would have so many dreams of me and him training together and stuff. And i'd roleplay about me and him winning the Johto League when I would play outside with my brother.
I was just obsessed with that dinosaur haha. I felt my bond with him was like Ash's with Pikachu's pretty much.....
....I miss bonding with my pokemon on my games like that xD; I think I had a good bond with my whole sapphire team, too. Like Meganium, I often fantasized about battling and training with my Blaziken too. It was fun :)
On 'newer' games, that I had more so in my adult-ish years, well......I'm not so sure I bonded so much with my pokemon. And....Now its all about my bond with Korrina xD