I had the same problem with my client wanting to change the color of the font all the time. In the contents_update_ContentValue1.php and contents_insert_ContentValue1.php files look for the line FCKConfig.ToobarSets["Custom"] (it's around line 16)
you can enable or disable any options available by removing say 'Style' (including the single quotes) and this will remove it from the menu. You can also rearrange this to your liking by reordering them.