Krokorok. I love the entire Sandile line, but it just has my favourite design.
Aside from that, though, I have a close bond with some 5th Gen Pokemon, both due to and not due to Nuzlockes:
Zebstrika: I never actually expected to be so fond of something like Zebstrika, but I am. It has an amazing design, is fast and powerful, and overall a great early game Pokemon. Honestly, if I ever replay 5th Gen again casually, I'll probably end up using a Zebstrika on my team due to how many great experiences I has with Misfortune in White 2.
Sigilyph: This thing is incredibly underrated for ingame. It has good enough stats to last you an entire run, and downright amazing coverage that makes it a very versatile member of the team.
Unfezant: It's no Staraptor, I'll give you that, but it's an early bird that's capable of lasting an entire run if you give it the right moveset. Its design is a rather appealing mix of simple and charming, so even if it doesn't stand out looks-wise, that's good enough for me. (Plus Unfezants have happened to be the only early birds that have ever lasted to the end of a Nuzlocke for me.)
Darmanitan: Darumaka may be a real pain to train, what with Hustle and all, and I may have had bad blood with it in the past due to how deadly they are in the wild, but training one up is well worth it. Darmanitan is incredibly powerful, and a real joy to use.
Seismitoad: I don't know what it is about Seismitoad, but compared to a lot of people who find it absolutely hideous, I actually think it's so ugly it's actually kind of adorable. Plus I had a really surprisingly good experience with it in my Black Nuzlocke- my Seismitoad, Metronome, essentially became my team leader due to being usable in so many situations, and was my choice to fight N's Zekrom. And she lived. And she had a Calm nature. Honestly, that secured Seismitoad as a permanent favourite of mine. If it wasn't for Krokorok, Cobalion and both dragon-types, I'm sure Seismitoad would actually be my favourite Unova Pokemon.
And I'm the only one here who likes it, apparently. I expected as much, but I would love to see more love for it.
Haxorus: It's an axe dinosaur. Enough said.
Cobalion: This one's simply due to nostalgia. I found Cobalion without even meaning to on my first playthrough of Black, and it ended up being better than I'd ever hoped. Ever since, it's been one of my favourite legendaries.
Sawsbuck: A Sawsbuck was the first Pokemon I ever EV trained, and it just has a really nice design.
Hopefully I'm not forgetting anyone. If I did, I'll update.