Mismagius, hands down! In fact, Mismagius is my favourite Pokemon overall! (No, it's not Ninetales. It WAS Ninetales before D/P came out, but Mismagius stole the show.) I love the way it looks and the kinds of attacks it can use...
Meh, I like Haunter better than Gengar for some reason...
Banette's my second-favourite Ghost-type Pokemon, and third favourite Pokemon overall.
I also really like Drifloon/Drifblim--they'd be a fairly close third behind Banette and Mismagius.
Dusknoir's pretty cool too, as is Rotom.
I always thought Sableye and Spiritomb looked kind of weird... but I kind of like them anyway.
Come on, Froslass?!? First of all, I HATE her English name. (Yukimenoko sounds a lot better IMO...) Secondly, I dunno... she just doesn't stand out to me.
Giratina... meh. Not my favourite legendary... besides, I never had one in the games, so I can't tell really.
Shedinja's awesome, especially with that Wonder Guard ability. I dunno why it never made it to my favourites list... but it didn't.