While I'd definitely suggest using hide instead of minimize, there is a way to unminimize windows from the application switcher (Command+Tab), it's just totally unintuitive. Here's what you do:

1. Minimize a window (Command+M). 2. Switch applications (Command+Tab). 3. Switch back to the application with the minimized window (Command+Tab). Before you release the Command key, hold down the Option key. Now release the command key.

Voila--your minimized window will return from the dock.