My favorite stories to write have been the Nick cancer stories and my collabs, especially Undead and 00Carter. I was really emotionally attached to Broken and BMS. I wasn't as attached to Curtain Call, but I still loved writing it, loved the reaction it got, and love the way it turned out. Almost all of my collabs have been fun to write, even the ones that eventually fizzed out - I love the interaction with my co-writers, the fun we have just throwing ideas around and planning the stories, and the crazy stuff we come up with that I never would have been able to think of on my own, let alone bring to life.
My least favorites are mostly older stories that aren't on AC: Silent Desperation, The Other Child, and One Night are the first three that came to mind. Secrets of the Heart wasn't a picnic to write; I loved the idea of it, but never really loved writing it... I'm glad I finished it though.
As far as readers' feelings, it varies. The Nick cancer stories were all amazingly popular, for reasons I'll never totally understand. Undead has done well. 00Carter not so much. And sometimes stories that I'm not as into writing, like Guilty Roads, are the ones that people beg for updates on. (I still like GR, don't worry.) You just never know!