If you want to clear all favicons from your bookmarks in Firefox 3, edit the places.sqlite database, which can be found in your profile folder, located in your user's Library » Application Support » Firefox » Profiles » random_text.default folder. You then need to use any SQLite editor to execute these two commands on that file:

delete all from moz_favicons
update moz_places set favicon_id = NULL

Quit the editor and restart Firefox, and the favicons will be gone (this works on every platform). Also, if you want to permanently disable favicons, type about:config in the URL bar, and edit these two properties:

• browser.chrome.favicons -- set to false
• browser.chrome.site_icons -- set to false

[robg adds: You can use the built-in sqlite3 program in Terminal to edit this file. Just cd into the profile folder, then (with Firefox not running) type sqlite3 places.sqlite. I had to change the format of the first command, however, to make it work in sqlite3 -- I had to remove all, leaving just delete from moz_favicons. After running both commands, type .quit and restart Firefox. This seemed to work for me as described in the hint.]