Change gnome taskbar icons

i have one question: i applied an icon theme , but some icons , like firefox or thunderbird in the taskbar does not change. Is this because they read the icons from another directory?

Not all icon themes have replacement icons for Firefox, Thunderbird etc so they won’t change and there may well not be a replacement in the icon theme directory.

As far as panel icons go you can always apply your own custom icons by rıght clicking on the shortcut and choosing properties then click on the existing icon and browse to the one you want. PNG Factory have a nice selection.