Thought I'd consolidate the side effects and synergies I've been seeing in play so far. I've got:

Dead Cat - When The D3 removes Dead Cat, it only removes one of the nine extra lives. This makes Dead Cat a very nice buffer if you're already in a good position!

Halo of Flies/Pretty Fly pill - The "fly" orbitals from Halo of Flies are each counted as a separate collectible instance, so The D3 only removes one of the flies each time. That's extra value!

NO! trinket - pushes the value proposition closer to even. The D3 can only remove your passive items, so guaranteeing that you'll only spawn other passives means you won't lose items to books you don't want. Plus, you can always drop the trinket when you want to farm for Guppy items!

That weird secret room with the Restock Box in it - because The D3 spawns a new item pedestal, you can reliably get use out of the Restock Box when you find this secret room variant!

Anyone have any other good ones?