Of course, 13 hours worth of narrative is a lot of information to sift through and, seeing as the show is chock-full of minor/obscure references, I've no doubt missed or omitted a great number of them. However, to keep this list as complete as can possibly be, I'll continually update it if more secrets are discovered or brought to my attention.
With that being said, here's a complete list of easter eggs I've either found or heard of, in the chronological order that they appear in the show.
*WARNING*
SPOILERS AHEAD
Atlas
At multiple points throughout the series, the office adjacent from Nelson & Murdock can be seen sporting a logo that reads "Atlas Investments." The design bears a striking resemblance to the logo of Atlas Comics, the real-life company that would go on to become Marvel Comics during a rebranding in the early 1960's.
Carl "Crusher" Creel
In Episode 2 ("Cut Man") Jack Murdock is booked for a big match with a man only referred to as Creel. A closer examination of the posters around the gym confirm this to be Carl "Crusher" Creel, a boxer from the comics who goes on to to become the super-villain known as the Absorbing Man.
Bullseye
This one is a bit of a longshot, but popular speculation is that the sniper that shoots Detective Blake in Episode 6 ("Condemned") is our first look at the classic Daredevil villain Bullseye. I personally didn't catch this one on my first viewing, but it would certainly explain why one can see what appears to be a playing card in his bag.
"The War"
Throughout Episode 7 ("Stick") Stick continuously refers to an ongoing "war" that he was trying to prepare Matt for. This war is briefly mentioned once again when Daredevil fights Nobu in Episode 9 ("Speak of the Devil"). In the comics, Stick is the leader of a secret warrior group known as the Chaste, that has rivaled a secret ninja society known as the Hand for many generations. Although neither the Hand nor the Chaste are ever directly mentioned, it is heavily suggested that their rivalry has always been in play even in the MCU.
Also, Nobu's attire during the fight in Episode 9 is a blatant reference to the uniform worn by Hand ninjas in the comics. I think by this point it's safe to assume that Nobu is the first Hand member we've encountered in the MCU, and I have no doubt his superiors will play a bigger role as we progress deeper into Daredevil lore in future seasons.
Elektra Natchios
Episode 10 ("Nelson v. Murdock") features a plethora of revealing flashbacks, one of which indicates that Matt took Spanish in college only to get closer with an unnamed Greek woman whom Foggy describes as "smokin'." Although this is a far cry from confirmation, it is widely believed that the Greek woman is none other than Daredevil's on-again, off-again love-interest/arch-nemesis Elektra, who is of Greek descent in the comics. She was also originally trained by Stick, who was introduced earlier in the series. And seeing as she goes on to become one of the lead assassins of the Hand, this season has done plenty to pave the way for her official introduction to the MCU.
Roxxon Energy Corporation
In another flashback from Episode 10 ("Nelson v. Murdock"), the law firm at which Matt and Foggy interned is revealed to have at one point represented the Roxxon Corporation. This might be a rather obscure reference for most viewers, but comic book fans may recognize this as the name of a massive, ethically shady corporation from the comic book continuity. It had also been passively mentioned at other points throughout the MCU, including the Iron Man trilogy.
The Steel Serpent
This symbol could be seen on all of the heroin throughout the show, but it was really put in focus when Daredevil brought it to the attention of Ben Urich in Episode 12 ("The Ones We Leave Behind").
Hardcore Iron Fist fans such as myself will probably recognize this symbol as that of Davos the Steel Serpent, one of Iron Fist's most prominent villains.
Later on in Episode 12, Madam Gao tells Leland Owlsley that her home is "a considerable distance farther" than China. Aside from packing her drugs with a Steel Serpent label and managing to knock Daredevil on his butt, this is our biggest hint that she's an otherworldly native. But from where? Ku'n Lun? Ku'n Zi? Is she working with Davos? Crane Mother? Both? She mentions that the heroin business is not her primary purpose for being there, but then what is? Is she simply establishing the Steel Serpent's presence on Earth? The enigmatic Madam Gao and her business leaves us with plenty of unanswered questions. There are only a few things we know for certain: (A) Madam Gao is definitely from one of the seven capital cities of heaven, and (B) It's still possible that they are looking to base the upcoming Iron Fist Netflix series mostly on the Immortal Iron Fist by Ed Brubaker and Matt Fraction, in which the Steel Serpent plays a very big role.
Whatever the case may be, the set up they do in this show has gotten this Iron Fist fan excited!
Gladiator
In Episode 11 ("The Path of the Righteous") Daredevil faces off against Melvin Potter, the man who was introduced earlier as the designer responsible for Wilson Fisk's armored suits. We also see him providing the same service for Matt when he later designs the iconic red Daredevil outfit. In the comics, the name Melvin Potter is also synonymous with a super-hero costume designer turned villain named Gladiator. As depicted above, one can see evidence of him designing the Gladiator suit in his shop during Episode 13 ("Daredevil").
Stilt Man
It seems Melvin Potter's workshop is a haven for easter eggs, as a prototype for Stilt Man's legs can also be seen in the background of Episode 13 ("Daredevil").
Stan Lee Cameo
It was a lot easier to miss, but it seems Stan Lee's tradition of Marvel cameos lives on. Though the legendary Silver-Age writer is usually given a walk-on role with at least one line, this time he was limited to a framed picture in the background of the police station in Episode 13 ("Daredevil").