The Angry Joe Show features several appearances by one of Angry Joe's friends, also named Joe. To distinguish between the two, he's often referred to as "Other Joe."
The Chairman's Ear: Averted, since the characters are all ersatzes of real-life politicians, almost exclusively referred to by their first name. There are two Jarosławs (the Chairman and the Deputy PM), two Mariuszes (the Chairman's assistant and the coordinator of the secret services) and two Donalds (the Chairman's rival and the president of the United States).
CollegeHumor has an entire video on the subject (in real life). Specifically, a video telling parents to stop naming their children Mike (or Michael) because of the absolute fuckton of Mikes in the US, and the only result will be that people give him nicknames, or use his last name. The video is narrated by Mike Trapp.
Three NPC characters in have very similar names — Shaun (usually called by his surname Gilmore), Shane, and Shauna. Not to mention Vax and Vex the PC twins (although those are shortened versions of Vax'ildan and Vex'ahlia, which are less similar), which causes a great deal of confusion when people try to address one of the twins in particular.
Sam: If I ever have to roll a new character, I'm calling him "Vix". Matt (DM): I will cut you.
The first episode of the Wildemount campaign introduces a PC named Beauregard, and an NPC named Bo'sun, who go by Beau and Bo respectively, resulting in some occasional confusion.
This happens across campaigns as well: both campaign 2 and 3 had a bad guy named Ira, with no relation to eachother. Campaign 2's Ira is one of the Somnovem, while Campaign 3's Ira is the Arc Villain of the first arc, also known as the Nightmare King.
When they attempted to play a Japanese copy of Drakkhen that a fan sent in, they couldn't read the characters' names (or indeed anything else), so they made up names for them: Brian, Bill, Langley, and another Bill. Also known as "Big Bill." And the first Bill might be a woman; they weren't sure.
One semi-famous Game Grumps skit was the 'Two Steves Show', which stars two hosts (played by Arin and Dan mimicking surfer accents) whose sole character trait (and joke) is that they're both named 'Steve'.
Arin: Tune in for the Steve Power Hour... It's tomorrow at three, 'cause it sounds a little bit like Steve. Dan: Yeah... 'Threeve'. Check it out at Threeve PM.
Gamers Nexusdoes only have one Steve, but as the site expanded, they've otherwise broken the trope by hiring two Patricks.
Jreg: The video "Leftist Infighting" introduced a character named Post-Left to moderate a debate between Ancom and Commie but by the end of Centricide 3, Ancom has become Post-Left as well.
Two of the cast members of Midnight Screenings are named Brian (last names Lewis and Irving). To get around this, Brian Irving was referred to as "Virtual Boyd" in early reviews before choosing to go by just Irving.
New Life SMP: As confirmed in her 2nd episode, Shelby knows an otter called "Pearl" that can help her crack open clams and obtain pearls; when fWhip asks, Shelby has to clarify it's not "the Australian Pearl", i.e. PearlescentMoon the creator-character.
The Nightmare Time episode "Abstinence Camp" features two camp counselors, Boy Jerry and Girl Jerry, and their son Little Jerry.
Out With Dad'': Averted. First there's Rose's friend/crush Vanessa, then she also dates another girl with the same name, whom they call "New Vanessa", and later nicknamed "Nessa".
SMPEarth has three Jameses: Jameskii, James Marriott, and RoastedJames.
In the SuperMarioLogan series, there are two characters named "D-Money"; A gangster kid who is one of Bowser Junior's classmates in the "Bowser Junior's First Grade" mini-seriesnote His real name is Demetrius, and a boxer who is Rosalina's ex-boyfriend.
Tales From My D&D Campaignhas the adventuring party recruit Daggerface, a dwarf driven insane by torture. They are very confused when they later learn they are being pursued by a bounty hunter named... Daggerface. The hunter turns out to be a warforged (magicpunk robot) whose face is literally a sextet of protruding blades.
(in real life). Specifically, a video telling parents to stop naming their children Mike (or Michael) because of the absolute fuckton of Mikes in the US, and the only result will be that people give him nicknames, or use his last name. The video is narrated by Mike Trapp.