Thunderbird on Windows always seems to pick up a good default font size for the message-list and tree panes. On Linux it picks some god-awful small font that, after a few hours, starts to make my eyes ache (and when one's sister is just getting over an eye infection, bloodshot, watery eyes tend to make her nervous that she's infected one).

As with many things in Thunderbird, this is controlled, not by a user-selectable option, but by a configuration file (a CSS file, actually) stored in a location where 90% of users will never find it.

Anyway, for the record, you add/edit the $profiledirectory$/chrome/userChrome.css file and insert this text (or something like it, it's regular CSS) to get a size that we whose eyes are already tired can see:

/* Messagepane text */tree {
    font-size: 14pt !important;
}

Happy reading.