The reason I came to like her in third-generation Pokemon was because of an old browser-based game called Pokemon Crater. It doesn't exist anymore because Nintendo apparently shut them down for copyright reasons. From how I understand it, though, they gave the creators of the site money to sell them the domain name. If you try to go to pokemoncrater.com now, it goes directly to the Nintendo website.
On this game, there was a bug where you could train ghost Pokemon all the way from level 1 to 100. It had to do with one of the Elite Four Trainers, Bruno. Because only one of his Pokemon, Hitmonchan, had an attack that could hit ghosts, you could literally grind a level 1 Gastly to a level 100 Gengar just by fighting Bruno. It was very silly.
I had teams of Gengars, Dusclops, Bannettes, Sableyes, and of course, Misdreavus. Because of how easy it was to build level 100 Ghost Pokemon on Crater, they became among my favorites. But Misdreavus has a special place in my heart. I think I just really like the whole design of her, and her mischievousness and all that. Plus, it's super cute!
I really like Mismagius, but I think it looks so witchy compared to the adorable Misdreavus. Still, Mismagius is a good Pokemon that has served me well since fourth-generation, so I like her just fine, too!
Oh, how I miss Crater...
Photo Credit: http://bulbapedia.bulbagarden.net/wiki/Misdreavus