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When switching between running applications via Command-Tab one can see all of the currently running programs.

This is however somewhat cumbersome, for instance I don't want certain programs to be listed there, say Adium - I would rather click on the icon in dock to bring it up, since I need it not as often as other apps.

I guess the solution I am looking for is similar to the behavior apps minimized into Windows tray area - can I somehow have an app running on Mac Os, active in the dock but not in the list of switchable apps?

It should be possible from technical standpoint - there are windows which not registered in the Command-Tab list, for instance - Character/Keyboard Viewer.

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This may not help you at all, but there a program called Dockless that allows you to hide an application from the Dock. Unfortunately, I think it hides the menu bar too. Depending the exact situation, this may or may not work for you. Hope it helps though!

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Alright, so I found as program called "Witch" which may help you. It's got a free trial on the website, but it does eventually costs $14. Check it out, it's got support for removing certain apps from the switcher and some other nifty features.
Website: http://manytricks.com/witch/
App Store: https://itunes.apple.com/nl/app/witch/id412485838?mt=12

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