I've always wanted to read Pinoko's Mystery. It sounds so delightfully bizzare!
I haven't read enough yet, but A Woman's Case was always one of my favourites. So sweet... and it has some wonderfully twisted humor ( nothing downplays a lewd husband fighting with his wife like drawing him as an actual pig ).
The Painting is Dead was very powerful. I really loved it.
Just about any chapter that pits Kiriko and Black Jack together is bound to be entertaining as well!