The Mozilla Application Suite allows the user to customize the colour of hyperlinks. This setting also affects email and newsgroup messages. However, because it is a browser setting, the options panel for it is not in Mozilla Thunderbird. Once again, this is one of those things that you can change in Thunderbird, through hidden settings.
The best way to do it, is using the AboutConfig extension, who’s function will be part of the upcoming Thunderbird 1.5.
To figure out what colours you want, open a message composition window in HTML mode. (If you see a toolbar that lets you change the font, size, colour, etc., you are in HTML mode. If not, hold down Shift, as you click on the Write icon.)
Open the colour picker.
Pick the colour you want to use, and copy the HTML colour string, at the bottom.
Now open AboutConfig [Tools -> about:config], and look for the setting browser.anchor_color. Double-click on it, and change the value to the HTML colour string you copied earlier. Click OK, close the about:config window, and you’re done.
If you ever want to change the setting back to the default, right-click on the setting in AboutConfig, and select Reset.
Some additional notes:
The setting for unvisited links is browser.anchor_color
The setting for active links is browser.active_color
(Since Thunderbird doesn’t have a browser history, there are no such thing as visited links in Thunderbird)
You can also change these settings using a user.js file, as described here.