Sending Applications to the Tray on Linux
Update (23 October 2007): A Spanish translation has apparently been made available at Blux 2.0.
If you want to have a clean taskbar on your Linux box, there are several different options. This is especially nice for people who aren't as fond of virtual desktops, or only use two or three. I personally prefer to only have my music player (which varies from time to time) minimized to the tray.
KDocker
KDocker, despite the K in its name, can be used on a variety of desktops. It is available as kdocker in Ubuntu.
KDocker is surprisingly easy to use. First, you start KDocker. I suggest creating a shortcut to launch it, by editing its entry in the Menu Editor if you're on KDE (Right click on K Menu, Menu Editor). You then are given a new mouse cursor where you can click on a window for it to be sent to the system tray. Below, I sent the Drivel window I was using to type this entry to the tray.

You can then click the icon in the system tray to have the window back. Once you have one application docked, you can easily dock more applications from any docked windows. You can also have a docked application go the dock whenever you minimize it. All of these settings take place when a docked application is right clicked.

KDocker is my personal favorite, but everyone has different preferences.
AllTray
AllTray seems to be more GNOME centric, but like KDocker, it works on a variety of Window Managers. It is also avaiable in Ubuntu as alltray.
AllTray first greeted me with a Window to configure the software, which I found quite peculiar.

Nonetheless, AllTray is quite similar to KDocker. Once you load the application you simply click the window you want and it wil go to the system tray. However, you have to load it each time you want to make a program go to the tray, leading to more of a need for a system tray. The options are also quite sparse, as you can see below.

Summary
Overall, these are both good applications. KDocker is more featured and uses slightly less memory, but if you want something that just works without any bells and whistles, then AllTray may be for you. If you use a similar application, I'd be interested to hear about it.

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Sweet!
I hadn't heard of KDocker before… very useful.
@The Geek: I'm glad you found it useful. Unfortuantely a lot of good applications remain unheard of to most people.
Very nice, I'd been looking for an app to do this. Being it was Kdocker, I avoided it thinking it wouldn't work for Gnome. I know.. noob mistake. Thanks for the post.
@Web Hosting: Nowadays about everything that can run in GNOME can run in KDE and vice versa. A while back this could be more problematic. Thankfully those days are about over (except for what Beryl and Compviz Fusion are starting).
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Very useful ur post, I translate it into my blog

A few day ago I knew your blog and it's excelent. Congrats
@CristianPC: I'm glad you liked the article and appreciate the translation
I do request that you leave me a comment on the article or drop an email to jatecblog@howtogeek.com before publishing a translation in the future though.
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I've used both applications.
The issues I have found with them is that they don't remember which applications you like in the dock. Having the ability to always put certain applications in the dock would make either of them phenomenal.