Normally, when you cycle open apps with Command+Tab, if you land on an application that has minimized windows, nothing happens. The way to remedy that is as follows: Hold Command and tab to the app you want to un-minimize. Without letting go of Command, press down Option, then while holding down Option, let go of Command.
It's a little awkward to use at first, then you'll do it automatically. I hold Command with my thumb, then tab with ring finger, then just move ring finger back down to Option, and let go of thumb.
Edit: Bonus tip: When landing on an application icon with Tab, continue holding Command and use Tilde (~) to cycle through windows of the same App. I use that one a lot too.