I came across a couple of Pokemon comics today that I thought were pretty cool and worth passing on. (Thanks, Reddit!) Both are fairly dark, but they're also pretty different in tone.
Pokemon Noir - pretty much what you'd anticipate. Like a Noir movie, but with Pokemon. Not a whole story, just several pages.http://imgur.com/a/vEKMS
"It's a Hard Life": a long comic with great watercolor art, made in the style of a "Nuzlocke run." (Rules are: if a Pokemon faints it dies, only catch the first pokemon in each area, name everyone.)
The actual site is really slow, but the artist posted faster links to chapters 1-7 on this forum.http://s7.zetaboards.com/Nuzlocke_Forum/topic/8538857/1/
When you're done, you can find chapter 8 on the artist's own site. It appears to be an ongoing thing, because the last page of chapter 8 was just posted yesterday.http://itsahardlife.smackjeeves.com/comics/1615318/chapter-8-page-1-cover/