Magmar > Magmortar
I remember the episode of the anime, 'Volcanic Panic', where Blaine of Cinnabar Island unleashed his badass of a Magmar. Ever since, as much as I do like Magby and Magmortar, I've always loved Magmar the most; in fact I almost wish that Magmar had remained an evolutionless Pokémon.
Misdreavus > Mismagius
Ever since I first saw Misdreavus at Mt. Silver, back when I got Pokémon Crystal, I've loved it. I'm a huge fan of Ghost-type Pokémon in general, but along with Shuppet/Banette and the Gastly/Haunter/Gengar lineage, Misdreavus remains a particular favorite. I recall being quite excited when I first heard the announcement that there would be an evolution for Misdreavus in Generation IV; alas, I was rather disappointed with Mismagius. Not that I don't like Mismagius, I do, but it just doesn't compare with Misdreavus in my mind.
Drowzee > Hypno
I'm not precisely sure why... I do recall that I thought that Drowzee sounded like a telepathic pimp in the anime, and actually had some amazing powers (e.g., the episode where a Drowzee is actually able to somehow control the minds of every single Pokémon on the island it was on); whereas Hypno just sort of sat around swinging its pendulum like a retard, repeating 'Hypno' in a bland, monotonous voice. Plus... I've never really understood what Hypno is based off of. I mean, obviously it's based off of the mentalist hypnosis trick with the pendulum, but why is he bright yellow with a white ruff and a big nose? It doesn't make much sense to me. In contrast, Drowzee is based off of a tapir, specifically, the baku, or dream-eating supernatural tapir of Japanese folklore. Which is cooler2.
Porygon & Porygon2 > Porygon-Z
No particular reasoning behind this one I suppose... I just don't like Porygon-Z as much as its preevolutions.
Dragonair > Dragonite
I've always liked the sort of elegant, majestic look of Dragonair, as opposed to the, frankly, chubby-tubby look of Dragonite. Don't get me wrong, I like Dragonite, a lot. I've simply always preferred Dragonair. It's more... mysterious. It has more of a feeling of mystery, of sleekness, majesty, elegance; I like that in a dragon. For this reason, Dragonair is one of the few Dragon-type Pokémon that really satisfies me (Flygon being a rare example of another).