There is one more but it's really subtle (Season 4 Krypto).

I remember the
Krypto episode, at least, sort-of. I re-read your story again and I'm still not seeing it. The first episode of S4 if one of my absolute favorites from Smallville - for one very obvious reason with the initials LL - but
Krypto is not a particularly memorable episode.
So, do I have to pull out the S4 disks and watch it or are you going to throw me a bone (sorry, I couldn't resist) and tell me the reference?
Bob