In the following sentence, should I use in or on?
If I ever make a list, not only will you be in/on it, you'll top it, too.
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You should go with on. I would phrase your sentence
If I ever make a list, not only will you be on it, you'll be on top of it.
On just-the-word you can take a look at many examples. For instance:
The first number on the list was a posh-sounding hotel.