The correct sentence is:
2. Make sure to put this movie ON your watch list.
Here's why:
"On" is used when something is added to a list, schedule, or agenda. The idea is that you're adding the movie to a list that exists as a metaphorical surface, like writing a name "on" a piece of paper. In this case, you're putting the movie on your watch list.
"In" is generally used when something is placed inside a container or enclosed space, which doesn't fit the concept of a list.
So, we use "on" for lists, agendas, or schedules.