When the webcomic The Noob parodied the "Time Warp" song from the famous stage play and 1975 comedy movie The Rocky Horror Picture Show in its episode #299 "The Dungeon Lifecycle", a fan on the comments board claimed that the webcomic was ripping off the MMORPGCity of Heroes, because they had used the "jump to the left" joke first; naturally, this came from a CoH mission packed with RHPS references.
Similarly, a fan asked on the comments box whether the "Eldritch Blob" monster was a reference to "Eldritch Deathlord" from Warcraft 3, not knowing that the term eldritch is dated by Merriam-Webster online to the year 1508. Horror writers like Edgar Allan Poe, Clark Ashton Smith and H.P. Lovecraft were very fond of the word, and it is from these that its modern use in fantasy comes.
The concept of romance applying to four separate types of relationships, only one of which being romance as we typically think of it, was first proposed by C.S. Lewis, who based his ideas on ancient Greek philosophy.
In general, troll culture is commonly thought to be an entirely original invention. While it can't be said for sure if any of it was intentional, many aspects of troll culture are very reminiscent of S.M. Stirling's The Draka, the Dremora civilisation from The Elder Scrolls (who even use the same alphabet and look very similar to trolls in physical appearance), and real-world Sparta.
The theme song of the Midnight Crew, "I'm a Member of the Midnight Crew", is commonly believed to have been written for the comic. It was actually written by vaudeville singer Eddie Morton in 1909, and the Midnight Crew are named after it.
Some readers, especially of the younger type, are unaware that the trolls' symbols are alchemical symbols associated with signs of the Zodiac and not an original creation.
Say "Put the bunny back in the box" to someone and they'll probably think you're referencing Homestuck. In fact, Homestuck got it from Con Air (and the line is even triggered by examining a Con Air poster).
In one strip of XKCD, Randall Munroe points out how people have complained about The Pace of Modern Life since the dawn of the 20th century.
Most webcomic fans consider US Angel Corps to be the first Western guro comic, which is wrong. Not only does the guro webcomic Alice in Neverland predate it by 2 years, but guro comics, at least under the definitions commonly associated with them, predate the internet. A good example of this is the Italian erotic horror comic series Storie Viola, whose release date goes as far back as 1987.