I've found what I think may be a bug in Unity mode on VMware Fusion 3.0 where applications running in Windows do not appear in the dock if they are running with elevated privileges in Windows.
For example, I use a VM to do Windows development for work. If I run Visual Studio 2008 normally, it shows up in the dock as expected. If I am working on a project that requires interaction with Internet Information Services, I am required to run VS2008 with Administrator privileges (i.e. right-click on the shortcut, choose "Run as administrator" from the context menu, accept the UAC prompt). When I do this, VS launches successfully but does not show up in the dock. I have confirmed that this behaviour also occurs with other applications (Notepad, Notepad++, Command Prompt).
Can anyone confirm that this is a bug? I can't really see how this is the intended behaviour.
My setup is as follows:
MacBook Pro 15" (late 2008 - "MacBookPro5,1")
OS X 10.6.2 (32-bit kernel)
Windows 7 Ultimate 32-bit
I can confirm the exact same thing is happening to me. When running VS2008 as an administrator it does not appear in the dock when in Unity mode. Additionally, every OS X window on my screen appears above it, even if I click some visible corner of it to bring it to the foreground.
Macbook Pro 15" Mid-2007 (3,1), 2.2GHz
OS X 10.6.2
Windows Vista Home Premium 32-bit
~1.5 GB RAM.
My workaround is to run the guest in a full screen on one Space, and keep my OS X stuff in another space, but this is far from ideal.