Are you using KDE? When I run Kopete, it minimises and sits in the system tray. Do you have a system tray? If not, right-click on the panel, select add->applet->system tray. Hopefully it will be there.
If you don't want a system tray, you can then bring it up by clicking on it and set it not to appear in the system tray and not start up hidden. Then you can remove the system tray