This snowclone goes back to the 1611 King James translation of the Bible, Psalm 23, verse 5, “Thou preparest a table before me in the presence of mine enemies: thou anointest my head with oil; my cup runneth over.” The original version implies gratitude to a higher power (“thou”) for life’s plenty. Modern variants are more likely to carry a sense only of “too much” and not allude to this gratitude.
Cup is the most common variant, including words that look like it (cpu), contain it (cupcake, D cup), or have a sense of containment as a cup does (chalice, pint, cranium, quarter jar, trough). Other variants include:
calzone
stash
optimism
discomfort
kennel
schedule
rage
teepee
It seems that modern users of this snowclone do not limit themselves to the more strict meaning of physical overflowing that “runneth over” is meant to indicate, but since the Psalm itself is meant to be metaphorical (you don’t have to have a real cup literally overflowing to say “my cup runneth over”), this seems perfectly natural.
The Snowclones Database 
It is not “perfectly natural” in any context to say that a kennel or teepee runneth over. It’s just nonsense.
Is there something about “my cpu runneth over” that is more natural than “my kennel runneth over”? Taken in context, the latter seems pretty easy to interpret, if a little twee. I think “my rage runneth over” is much closer to nonsense than any physical object with a sense of containment, which “kennel” certainly has.