1.
Londo/G'Kar - Babylon 5. These two characters essentially 'grew each other' in alot of ways, and therefore I don't think can be listed separately. They were responsible in large part for each other's growth, and both of them ultimately grew in a positive direction....although both got worse before they got better. Which I think only added to the growth.
2.
James "Sawyer" Ford - LOST. Sawyer started out LOST as what was quite possibly the most selfish, self-serving, hostile, and downright mean-for-the-sake-of-it characters ever to hit prime time. This was a guy who went out of his WAY to do the wrong thing, just to hurt someone for no reason at all other than that it increased his rep for meanness and hostility. This was a guy who TRIED to be hated.
I won't say too much for fear of spoiling n00bs to LOST out there....but these days, Sawyer is pretty damn near a loyal, stand-up guy who even puts his life on the line for his friends. But as a bonus, he has
not lost his quite formidable sense of humor in the process.
Interestingly, although others in this thread have listed Locke, I actually actively dislike his transformation and find him to be quite arrogant, bullying, and narrow-minded these days. I guess it's one of those transformations where 'your mileage may vary'.
Transformations 1 and 2 are so pronounced that it's barely worth mentioning any others. But I suppose some other ones would be -
Daniel Jackson - Stargate SG-1. Was always a nerd...but became a more 'socialized' nerd.
Kira Nerys - DS9. She became alot more trustful of the Federation...and alot less hostile in general as time went on.