There are actually some commercial pop up flash modifiers that are pretty creative in their designs.
The Graslon Spark fits over the pop up, reflects the flash back to a larger reflector, then diffuses that light to make the flash considerably softer.
Spark Pop-up Flash Diffuser
The Demb Pop up Flip-it reflects the flash upward to bounce off of the ceiling, and has an adjustable angle bounce card in back of the flash head to direct however much light you want forward or not as you choose.
Demb Flash Products - Demb Pop-up Flip-it! Flash Reflector
I like the Demb -- it fits in a pocket so I can have it with me at all times -- I found a little case that can carry a spare battery, memory card, and the Pop up Flip-it, so I just slip that into a pocket when I grab the camera. It's my all around photo safety net.
With the ability to use higher ISO without too much penalty, smaller flash guns with less power become more useful in more situations, and it doesn't get smaller or more convenient than the pop up if you can modify the light from it to be more pleasing. I'm using it and a very compact Metz 24 AF1 a lot more and leaving the big AF 540 FGZ home most days with the K-5 and K-5 IIs, but I'm more inclined towards less advanced use of flash than many.
Scott