um...throwing a few random ones out there:
Ordinary is about a female assassin, though I don't think it's episodic and it's pretty short (only 2 volumes)
Jormungand isn't really about a female assassin but rather a group of weapon smugglers with a girl leading them. She's not an assassin/spy herself but I'd say she is certainly brilliant in her trade, and the manga is somewhat episodic.
Black Lagoon - I haven't read the manga, only watched the anime, but she's a killer, so...but I suppose this one's mostly violence instead of wit