This was one of those rare episodes where every plotline traces back to an earlier episode, rather than the typical introduce-then-forget-new-characters formula the writers are so fond of. Gotham should try this method more often.
Using Commissioner Loeb as a big target, "Everyone Has a Cobblepot" brought together Gordon, Dent, Bullock, and Penguin for one unified adventure that felt good.
As more of a fan of the Nolan approach than, say, the Tim Burton or the old-school TV show versions, I appreciated the realism of most of this particular episode. It had a hardboiled detective novel or movie sense to it that really worked for me.
Luckily, "Everyone Has a Cobblepot" managed to stay a strong episode throughout by doing what Gotham does on its best days - it stayed really, really weird.