Mozilla's Firefox and Thunderbird are pretty bad offenders of this sort of thing. They don't seem to want to code an interface consistent with the platforms on which they run.

When you double-click on a word, that should select it. When you press a shift-option-arrow combination to select a word, it should select the word.

Eudora was the same way for a while. They finally put their preferences in the correct place, or at least had the ability to get to it from the correct place and the old, incorrect place.

Huh. On my Mac, preferences are always under [Program Name] > Preferences. What annoys me is that a few of my applications do not use the standard Cmd+Comma shortcut.

MacOS was designed with some pretty stringent UI guidelines back in the day, although they've been relaxed considerably, so there's a lot of consistency there.

Windows since XP has been more consistent but not as much.

Mozilla apps are cross-platform so don't necessarily conform to a given UI, unless they're redesigned for integration like Camino.

The Firefox "preferences" debate is never-ending. Programmers tend to like to configure everything, or make it an option, and making something an option is one way to settle a difference of opinion, so you end up with badly-designed abundances of prefs menus with the most obscure stuff having checkboxes.

I think every programmer out there decided what they liked with their first applicatino (like your favorite Dr. Who or James Bond) and won't change.

On OSX, virtually all apps are under [Program Name] including Mozilla/Firefox. If by back in the day you mean OS9, it was actually much less organized then and as far as I know, there was no prespecified place to put prefs. Sometime under File, sometimes under Edit.