Oliver Queen isn't actually called Green Arrow until Season 4. At first he's just "the vigilante" or sometimes "the hood", then "The Arrow" starting in Season 2.
The island on which Oliver is marooned, typically called Starfish Island in the comics, is renamed Lian Yu (meaning purgatory).
Dinah Laurel Lance goes by Laurel Lance, to differentiate herself from her mother.
Laurel's father, Larry Lance in the comics, is Quentin Larry Lance.
Star City itself is Starling City, until it's renamed Star City in Season 4.
Arthur King/Merlyn the Archer is Malcolm Merlyn/the Dark Archer.
In Season 2, Nyssa Raatko is introduced as Nyssa Al-Ghul (taking her father's last name), although her legal last name is still Raatko.
Michael Holt/Mr. Terrific is Curtis Holt.
Wild Dog's identity in the comics is Jack Wheller. In the series, he's renamed as Rene Ramirez, to accommodate his Race Lift from Caucasian to Hispanic.
In the New 52 comics, Ricardo Diaz Jr. used the name "Richard Dragon" as an alias. In Arrow, he is simply known as Ricardo Diaz and his codename is "Dragon."
The last two seasons of the show revealed that John Diggle is actually the Arrowverse counterpart of John Stewart.
Iris West's father's first name changed from Ira (New Earth) or William (New 52) to Joe.
Roy G. Bivolo goes by Prism rather than "Rainbow Raider" or his New 52 codename of "Chroma".
Peek-a-Boo has her name changed from Lashawn Baez to Shawna Baez.
The S.T.A.R. Labs founder's name is changed from Robert Meersman (Silver Age) or Garrison Slate (New Earth) to Harrison Wells.
The Reverse Flash's real name remains Eobard Thawne, but he spends most of the first season going by the alias "Harrison Wells".
Jesse Quick's real name is changed from Jesse Chambers to Jesse Chambers Wells, as she's the daughter of Earth-2 Harrison Wells.
Several examples stemming from the Gender Flip trope:
The Bug-Eyed Bandit is named Brie Larvan rather than Bertram Larvan.
The Top's real name is Rosalind "Rosa" Dillion instead of Roscoe Dillon.
Black Bison's real name is Mina Chayton rather than John Ravenhair.
The Fiddler's name is changed from Isaac Bowen to Izzy Bowen.
Spin was only known as "Mr. Auerbach" in the comics (his first name was never given), while in the show, her real name is Spencer Young.
Although the Earth-2 Mirror Master remains Evan McCulloch, his Earth-Prime counterpart is a woman named Eva.
Barry and Iris' daughter is named Nora instead of Dawn. She's also a Composite Character of Jenni Ognats, as she uses XS as her superhero identity. In the 100th episode, the Reverse Flash calls her Dawn, implying that was her name in the original timeline that he came from, making it an In-Universe example.
Connor Hawke's birth name is revealed to be John Diggle, Jr., as his father is John Diggle in this continuity.
In The Secrets of Isis, the title character's real name was Andrea Thomas. The comics had previously Race Lifted her as a Khandaqi named Adrianna Tomaz. Here, she's an Arab-American called Zari Adrianna Tomaz.
On Earth, Kara Zor-El goes by Kara Danvers instead of either Linda Lee or Linda Lee Danvers, names she used in the comics.
In the comics, the Daxamite Lar Gand is better known by his honorary Kryptonian name of Mon-El. In the series, Mon-El is his real name. His father, Kel Gand in the comics, is Lar Gand.
J'onn's brother's name is slightly altered from Ma'alefa'ak to Malefic. Although that was his "villain name" in the comics.
Fifth-dimensional imp Miss Gsptlsnz has her name changed to Nyxlygsptlnz, or "Nyxly" for short. (This comes from Action Comics (New 52) run, which introduced her as an apparent human named Mrs Nyxly.)
Morgan Edge turns out to be an alias used by a Kryptonian named Tal-Rho.
Natasha Irons has her name changed to Natalie in this continuity.
The Big Bad of the ElseworldsCrossover is called Dr John Deegan, but seems to be the Arrowverse counterpart of Dr. Destiny, whose real name in the comics is John Dee.
