Okay, I think I got this pretty much set up how I want it. FYI, for me, when I am in Mac OS X, I like the following mappings because the resulting layout matches the Mac keyboard: Alt -> Command, Windows key -> Alt/Option. But when I am in Windows, I want my keyboard to behave just as if I were on a PC.
Part of this solution is specific to the Microsoft Ergonomic 7000 Keyboard. That may make some of this info irrelevant to people who have other keyboards because the 7000 has software that can be installed on a Mac, which is actually pretty nice. But the other stuff might help guide you nonetheless. If you're keyboard is just being used generically (i.e. Alt -> alt/option and Win key -> Command), then skipping right to the next step might work just fine for you.
These are the other pieces of my setup: MBP with Retina, OS X 10.8.3, Parallels 8, and Windows 7 (Ultimate) imported from Boot Camp.
So here goes. I have the software for the 7000 installed which I had to download. It's called IntelliType Pro (version 8.2.0). Once it's installed it integrates into the System Preferences in the "Other" section. Open it. You see the "Global Settings" profile is selected. I don't remember what the default options were, but click Options, and make sure 'Swap Windows and Alt keys' and 'Reassign application key' (the context menu key) are checked. Now I've got my Mac keyboard layout.
Note: there is also a 'Swap Control and Caps Lock keys' option, but I honestly have no idea why you would want that checked.
Now, for setting up Parallels.
Still in the IntelliType Pro settings, we need a separate profile for Parallels. Click 'Add' near the top, and find Parallels Desktop to create a new profile for it. Click the Options tab and clear those two checkboxes.
Note about this: This will affect all of Paralllels Desktop, even when you're not "in" a VM. But when it's all said n done, being in Parallels probably means being in Windows. The minor drawback is that Parallels Desktop doesn't act like a regular OS X app in regards to keyboard shortcuts.
Next, in the Parallels Desktop Preferences, click the Keyboard tab.
In 'System Shortcuts', change the 'Send system shortcuts' setting to Always.
Explanation: This may not be necessary for everybody but if you use certain keys or shortcuts, Parallels might interpret that press as an OS X command, when you wanted it to be sent to and interpreted by Windows. For example, an app I use in Windows uses F12, which Parallels interprets to 'Show me the Dashboard'. This also has the drawback that you won't be able to 'Alt/Command Tab' out of Windows to OS X apps. I found a way to deal with this by using the Parallels Application shortcut (which is listed in the 'Application Shortcuts' section), Command + H. When you're in Windows, even in full screen mode, this will hide Windows and put you on whatever the last OSX app was that you were using. Then, to get back to Windows via the keyboard, you just Alt/Command + Tab back to Parallels Desktop (not a specific Windows app. That doesn't work, perhaps because we used Hide).
Still in Parallels Keyboard Preferences, click the particular VM that you're trying to "fix". Click in the Profile drop-down and click 'Edit profile list...'. Select the Windows profile, click the gear icon, and click Duplicate. Select the new 'Windows 1' profile as the profile for your Windows VM. Clear all the checkboxes for the key mappings "from Mac OS X to Windows".
The next two steps had already been done when I had my "viola, it works" moment. However, I'm pretty sure they are necessary for it to work.
We need to make one more Parallels config change to turn off an "auto keyboard swapping" "feature", but it's not available in the Preferences menu. Don't worry, it's pretty quick. Follow these instructions, which I found here:
Now, boot up your Windows VM. And follow rdlsmith's instructions which are posted above.
That's it. Hope that helps some people.
