As with many pages on this site (especially the comp sub-site), much of this is for personal reference. Much of this I won't have tried, but am making a note of in case I use it in future, other things I'm making a note of in case I reinstall software.
Profile folder default locations:
C:\WINDOWS\Application Data\Thunderbird\Profiles\default\xxxxxxxx.slt\ in W98x/Me;
%AppData%\Thunderbird\Profiles\default\xxxxxxxx.slt\ in W2000/XP;
~/.thunderbird/default/xxxxxxxx.slt on *nix;
~/Library/Thunderbird/Profiles/default/xxxxxxxx.slt on MacOSX.
user.js (various prefs) in profile folder. Does not exist by default. Type = text/plain (or maybe just text).
userChrome.css (program appearance) - located in chrome sub-folder of profile folder. Does not exist by default. Type = text/css.
userContent.css (mail appearance) - located in chrome sub-folder of profile folder. Does not exist by default. Type = text/css.
Making Thunderbird default mail program:
Windows / Mac - Tools -> Options... -> General in Windows and Mac
GNOME - Control Panel -> Document Handlers | URL Handlers mailto: gnome-moz-remote "%s" then find (or create) ~/.gnome.gnome-moz-remote and place text [Mozilla] filename=absolute path of Thunderbird install directory/mozilla;
KDE 3 - Control Centre -> Network -> Email -> Preferred Email Client absolute path of Thunderbird install directory/mozilla --mail