Windows Mail does not have the minimize-to-tray feature. But Kristan Kenny has written an software which will provide you with a way to control Windows Mail from the system tray as well as minimize it there.
You can download the utility from the following link:
http://www.msblog.org/download/WinMailTray.zip
Download the file to your Desktop. Unzip the contents to a folder of your choice. Then double-click WinMailTray.exe to run it. You may create a shortcut of the file in your Startup folder if you want the utility to run everytime when you start Windows Vista. To open the Startup folder of your user account, type the following shell command and press ENTER:
To hide the Windows Mail icon from the Taskbar, right-click on the WinMailTray icon in the Notification area and then click Hide. Here is the list of context menu items you see when right-clicking on the icon.

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Great little add but only found one thing wrong when you open windows mail to read your messages or anything else then minimize it when finish you have to right click icon and hit hide again, its a pitty as if it just stayed in there and you minimize windows mail it also hides to automatically like office outlook 2007 does.
Maybe some one will be able to do it as microsoft dont have the brains to do it as they would of done it by now.