- Be sure that the system tray icon of Pidgin is always shown, so you will be able to open the buddy list, if it is minimized (menu "Tools", then "Preferences"; "Interface" tab; "Show system tray icon" to "Always").
- Click on the Pidgin icon, in the "Buddy List" window titlebar.
- In the window menu, click on "Advanced", and then on "Special Window Settings...".
- In the "Window-Specific Settings" window, click on the "Preferences" tab.
- In the tab, check "Skip taskbar", and then select "Force" in the dropdown list, and check the box on the right of the dropdown list.
- Finally, click on the "Ok" button, and the taskbar entry for the Pidgin buddy list should disappear.
There might be similar options for the Gnome window manager, and maybe others.