-I don't know if it's too amorphous and un-magicky to count, but his kills in DB seem to haunt him during PG and beyond:
[Murph:]"You look like you're bleeding, somehow...you killed them. It's eating at you....You made the choice cold...[in reference to her own killing of Denton]...but it made me feel stained. To take a life." (PG, 99-100)
[Harry:]"I've never killed, man. Not like that. Cold."...[Michael, in response:]"You feel like nothing is ever going to be right again...you feel stained." (PG, 385)
-And I guess the obvious (if still unmagicky) one, manipulating/killing Susan in Changes: "One day I hope God will forgive me for giving birth to the idea that came next. Because I never will." (C, 415) "'It wasn't hard,' I said quietly. 'Just cold.'" (C, 425)
-And another unmagicky one where he doesn't perceive it, so this may be way too tenuous: his complete contempt for and utter brutality to ghouls. In terms of that counting as a stain, in a different context, he talks about how "Life's easier when you can write off others as monsters, as demons, as horrible threats to be hated and feared. The thing is, you can't do that without becoming them, just a little. Sure, Lasciel's shadow might be determined to drag my immortal soul down to perdition, but there was no point in hating her for it. It wouldn't do anything but stain me that much darker." (WN,276-277). Seems to me that's exactly what he's done with ghouls, despite his initial comments to Ramirez in the same vein as the quote above.
These nonmagical examples might not count; I'm not sure. I guess I never grasped why murdering by magic does more harm to the soul than just general murder. I get why invading someone's mind/free will does some terrible damage, but it seems to me that murder is murder, and it stains the soul, whatever the weapon.