The solution to your first problem (with Command-Q) is to enable the option in Parallels preferences->General->Perform Action when Virtual Machine is running... For "On application quite" set to "Ask me what to do". Then when you press Command-Q, a dialog will pop up and ask if you want to quit, suspend, or cancel. Problem solved.
To get Command-Tab to switch you from a Windows VM to a Mac app, you must disbale "enable access for assistive devices" in "Universal Access" (from System Preferences under Mac OS). This is a bug with Parallels. As some programs require this feature to be enabled to work, having to disable it is at best a work around, not a solution, but for the time being, it will solve your trouble with Command-Tab.
Rather than disableling the Comand-<key> combos in Parallels, instead, Parallels needs to make all Command-<key> combos pass through to Mac OS and not use this key for Windows (but provide the option to enable or disable the Command key as the user desires). Right now Command is acting as the "Windows" key which causes all sorts of issues like having the Windows Start menu pop up. Just as there are good reasons to prevent Command-Q from shutting things down, there are similarly good (better in my opinion) reasons to make sure Command-Tab or other Command-<key> combos gets you out of Windows and switches to or executes a Mac keyboard function.
I think if Parallels did two simple options, almost all Command key and keyboard focus issues would be resolved:
Option 1 - Enable Command as Mac "Command" key or "Windows" key
One or the other, not a halfway state like it is now. And, this must work regardless of the setting of "Enable access for assistive devices".
If set as Mac "Command" key, anytime Command is pressed, the VM should be defocused so that all keyboard _AND_ mouse funcitons work on Mac OS and are not passed to Windows. Pressing Command would also bring up the Parallels Mac OS menu at the top of the screen (in full screen mode) or cause keyboard/mouse focus to divert to Mac OS (in Windows/Coherance mode). This is exactly how Virtual PC works - simple and predicatable.
If set as the "Windows" key, then the Command key would work as the "Windows" key on a standard PC keyboard and would not be passed to Mac OS. Pressing the Command key would bring up the Start menu like on a normal PC. The only way to get keyboard/mouse focus back to Mac OS would be to press the CTRL-OPTION keys (or what ever keys you have configured in Parallels Preferences->Keyboard->Release Input.
Option 2 - Allow swapping Command and Option/Alt keys
When enabled, this would swap the functions of the Command(Windows) and Option(Alt) keys so they worked as normally found on a PC keyboard.
Of course, a fully configurable (no limitations) keyboard mapping preference item would be nice, but the above two options are a simple way to make things work with minimal confusion.
