Through the Looking Glass was written by David Kemper. David Kemper also wrote the Princess Trilogy, and Die Me Dichotomy. I believe Through The Looking Glass is a tremendously important episode. Much more important than I once thought.
Crackers Don't Matter was written by Justin Monjo. However, I also believe that this was a tremendously more powerful episode in terms of future plot lines than I once did.
The reason? Both feature Moya glowing.

In TTLG, much of Moya was being torn to shreds by the Inter-Dimensional Beings (IDBs), and those parts of her that were gone were replaced by a scaldingly bright white light. In CDM, T'raltixx altered Moya's bioluminescence (sp?) to make her glow. Those parts of her that were effected were giving off a scaldingly bright white light.
SO, what if T'raltixx was trying to alter Moya in such a way that she would slip between the bounds of the space-time continuum and into that place where the other IDBs live. Yes, I said "other". What if T'raltixx was a rogue IDB?
The Farscape writers know exactly what they're doing. They would NOT show us an IDB if it wasn't important to remember. And in CDM, T'raltixx made a comment just before John killed him about how, "there are thousands just like me! We will find another Leviathan to make our light! And when we do, we'll spread like a plague? We will rise from our dormancy and kill you all!"
Another interesting Item Of Note: Chiana said, in TTLG, that the Nebari weapons scientists actually poked a hole into the realm of the IDBs. It lost control and 4 populated planets were destroyed.
... but what if it didn't? What if the IDBs forced it out of control? Could Moya's crew have an inter-dimensional ally?
And what were the Nebari doing trying to mess with the Realm of the IDBs, anyway?