I LOOOOVE pencil skirts...I have lots of them. Probably too many. I like to dress mine down with a looser/more voluminous top and a belt around the waist. Something about an untucked top with a pencil skirt says "dressed down." I also like to keep a top tucked in but dress it down with more casual shoes (not pumps) and accessories, like big non-shiny necklaces (wood beads, etc.) or bangles.
Plus try matching a pencil skirt with more casual fabrics and patterns on top. Jersey, cotton, etc. instead of silk or tailored cotton.
One of my favorite outfits is a screaming hot pink below-the-knee pencil skirt from Anthro worn with a little pale blue plaid cotton button-up sleeveless blouse tucked in, with white and brown oxfords. Something about the cotton and the plaid in the top makes the whole thing very dressed down. It's fun. I can also dress that skirt up, although admittedly screaming hot pink is a hard color to pull off in dress-up occasions!