Yes, it can be
done! I was getting quite
annoyed that apps could not be
prevented from showing in the
dock when running. There are some things I don't want there, such as
wClock (a clock that displays in the OSX top bar where
God intended it to be!) and other things that should run in the
background. Now, there's an option to specify what
apps to start up on
login, and there's even a
checkbox next to it to "hide" the app, but that doesn't seem to do
anything other than get your hopes up. So here's what you do...
You can do this in the finder or in a terminal. In a terminal, cd to the app (OSX apps are actually directories containing binaries, icons, resources, etc and you can cd right into what the finder shows as an app) and open up Info.plist in your favorite text editor. In the finder, navigate to the app, and control-click (or right click) on the icon, and choose show package contents. Double click Info.plist and choose TextEdit to open it up.
In OSX, like NeXT, applications have settings that can be altered. Every app has a plist which specifies things like name, version, icon, type and creator, and interface binary. You should be careful, editing this can screw up your apps. The file is just XML with key and string pairs. We want to add the following:
<key>NSBGOnly</key>
<string>1</string>
Add this right before the </dict> tag, and save the file. This key specifies that the app should be run in the background only. Keep in mind, it won't be in the dock and it won't show up when you do command-option-esc, so you'll have to use the process manager or a terminal and kill to end the app should you need to. This should work with any app.
For anyone using OSX Beta, wClock can be found at www.wolfware.com/wclock.