@ahx I think it's down to personal preference.
Initially I used RDoc for the Mocha gem [1], because it was the only option at the time. However, I switched to Yard about 12 years ago, because it provides richer information about the code and I'm still _fairly_ happy with it.
I hadn't seen TomDoc, but at first glance it looks interesting.
@ahx One consideration might be if you want to rely on one of the sites that automatically generate docs for gems, e.g. https://rubydoc.info/. However, since I publish my own docs [1], this isn't an issue for me.
@ahx Also I think gem specification [1] still assumes you're using RDoc, although I seem to remember that Yard is backwardly compatible with RDoc...?