1. Thomas & Friends - Around the time Oliver started appearing less and less in Thomas & Friends until disappearing for several seasons the writers for some reason decided to reuse the name Oliver for a brown excavator (Though he was originally going to be called Buster which was later reused for a steamroller) Many years later they poked fun at this oddity in Sodor’s Legend Of The Lost Treasure where Marion the orange rail-mounted steam shovel who tends to have strange beliefs had believed they were one and the same due to thinking Oliver the engine made a wish to some small engines to turn into a excavator (And coincidentally enough one of them is called Bert which is also shared with a diesel although at the time the diesel was introduced they had no plans to bring that engine from the books into the show) The joke later on pays off in a really funny way where we actually get to see them both onscreen for the first and only time in that very movie near the ending of the movie something I never thought would ever happen.

2. Ultimate Marvel Vs. Capcom 3 - In this game there are two characters who have the name Phoenix, Phoenix whose real name is Jean Gray and Phoenix Wright the main character from Ace Attorney series. Hulk of all characters is the only one to point this oddity out in his quote to Phoenix Wright where he expresses confusion over how Phoenix Wright is not the “bird lady”. (Additionally on a somewhat related note Phoenix Wright is often referred to as Mr. Wright by other characters to avoid confusion) Although this joke only works in English since in Japanese his name is Ryūichi Naruhodō. 

3. Super Smash Bros. series - Roy and Roy Koopa (Who is an alternate costume for Bowser Jr.) in the Super Smash Bros. series and are notably the only playable characters to share the same name. This was poked fun at several times such as in Roy’s Classic Mode congratulations screen where he is shown alongside Roy Koopa (Which is the very image I am using for the characters both named Roy) and in Roy’s DLC trailer from Super Smash Bros. 4 where he attacks Roy Koopa to give himself the spotlight in trailer.

(Funny Trope) Two characters unintentionally sharing the same name and it being acknowledged and poked fun at in-universe