I love what this show is setting up.
Some of the more obvious ones - Catwoman, Bullock, Ed Nygma (Riddler), Ivy "Poison Ivy" Pepper and The Penguin were fairly obvious.
Also, a LOT of neat Easter Eggs from the comics.
The dancers at Fish Mooney's club were very obviously wearing Harley Quinn-esque outfits. If you're interested in her backstory, The Batman Adventures: Mad Love is a good read.
(Batman Adventures: Mad Love)
The "tougher" Alfred is probably inspired by Earth One Alfred - he was ex military.
(Alfred Earth One)
Mayor James is also from the comics, from before the Waynes were shot. From the "Madmen of Gotham" arc of the Legends of the Dark Knight comic. An obscure pull, the only time I can recall him being mentioned was in this comic which came out around the time of the original Batman movie.
(Madmen Of Gotham)
Lt. Essen was also in the comics, and has an interesting backstory, it won't let me spoiler it in this post so I'll post it in a second post.
She appeared in Batman Year One, and again later in Legends of the Dark Knight.
(Legends of the Dark Knight),
(Batman Year One)
"The Comedian" - as I mentioned earlier, if you read "The Killing Joke" - a possible backstory for the Joker was that he was a stand-up comedian.
(The Killing Joke)
Montoya and Allen are directly from the Gotham Central series of comics that focused a lot on Gotham Police.
(Gotham Central Comic)
The Roman (Falcone) was from Batman Year One. Also in the Batman Begins film.
(Batman Year One)
4th and Grundy was a neat nod to Solomon Grundy.
(Solomon Grundy)
Barbara Kean (future Mrs. Gordon) lives in an apartment that has a clock tower face looking out on the city. She eventually became Oracle and provided intel to superheroes. And her headquarters was in a clock tower, so a nice nod to that character.
If you remember in Arrow, Canary's headquarters was in a clock tower which was eventually destroyed. But Canary and Oracle had a series as well that's a good read.
(Birds of Prey)
And I didn't directly observe this but a friend told me in graffiti on one of the rooftops when the camera does a pan, you can see the word "Smile" spray painted in red (maybe a nod to the Joker). I'll be rewatching today to see if I can catch it.