Most of the nuzlockes I follow are already listed, so... I will put these two up:
- Land-walker's Yellow Nuzlocke: Although he, sadly, couldn't finish it, the plotline that he devised is amazing (he summarized the rest of it in 4 plot summaries with many details). Elements of real life and the manga version of Pokemon are incorporated in this story. You might need to read his original Sapphire nuzlocke (simply called Landwalker's Nuzlocke) in order to get the complete picture though. Both are enjoyable to read for me.
Link here: http://land-walker.deviantart.com/gallery/29972549/Yellow-nuzlocke
- Kittengoo's "Judgment" - A Heartgold Nuzlocke: I found her a long time ago when she worked on her first nuzlocke, but she took it down and replaced it with this one. Her art style is very unique and she isn't shy about addressing controversy and pushing the envelope.
Link here: http://kittengoo.deviantart.com/gallery/38508873/Judgement-A-HG-Nuzlocke