Character Names: Giving a character a name that is similar or the same to the name of the person you're referencing. For example, if you want to reference a person or character named Alice Williams, you might name a character "Amy Wilkins". This is hard to detect, and often requires confirmation by the writers. Even if their Name's the Same, it can just be a coincidence.
In-Universe Works: Sometimes, a Show Within a Show is a reference to a real-life show, as can be the case with other types of works. For example, Doctor Who might be referenced by having characters watching a show called "Doctor What". Sometimes, it's obviously a reference (for instance, that "Doctor What" example), but sometimes it's less clear. For example, if characters watch an intentionally bad horror movie, it can be hard to tell if the work is spoofing a particular movie or just B-grade horror movies in general.
Character Behavior: Having a character who acts like the person or character you're referencing for some reason. Like names (which it can overlap with), this can be hard to detect.
Scenes: Having a scene similar to a scene in an existing work. Again, this is hard to detect, but it's more likely to be a reference if someone says something similar to an iconic line from the work, mentions the title of a work, or mentions they've seen/read it in a work.
Music: A song or piece of music similar to an existing piece of music. The trope for that is Suspiciously Similar Song, but it's YMMV because the trope is hard to define.
Character Appearance: Having a character's clothes, hair or other things about their appearance be similar to the person/character being referenced. Can overlap with names and behavior and, like those shout-outs, it can be hard to determine if it is a reference.
Mentioning a Work Directly: For example, saying, "I saw it on an episode of [Show That Exists in Real Life]" or mentioning something/somebody that belongs specifically to that work (for example, lightsabers are unique to the Star Wars universe).
Mentioning a Work Indirectly: For example, referencing Star Wars by having a character mention "the movie with the moon that was really a space station". Often hard to determine if it's a shout-out.
Plots: Having a plot overlap with the plot of an existing work. Sometimes, it is hard to tell, but other times the plot is a blatant parody.
Dialogue: Saying something that references dialogue from another work or something said by a celebrity. For example, if Alice has an Italian accent and is famous for saying, "No way!", then someone might reference her by having Bob say, "No way!" in an Italian accent. Unless it's an obscure phrase, this can be hard to detect.
Actors Alluding to Their Other Roles: Can overlap with some of the other types, but can involve mentioning the role (directly or indirectly), another character pointing out that they look like another character they played, etc.