It would be cool if there were options in Esc -> Interface -> Addons -> LogTracker or another place to choose what to display in the tooltips. E.g., I'm only interested in showing 25man Naxx / OS / EoE logs so I would unselect 10man Naxx / OS / EoE and both 10man and 25man VoA.

Valid point, I'll implement is when I have some spare time :)

It is now possible to hide either 10 or 25-player logs. I'm not yet sure how best to solve individual raids without having to adjust the options with each phase. If I come across a good "general" solution I'll go for that, otherwise I'll just do it hardcoded for each phase.