Cmd+Tab for apps that are running but closed in Yosemite
If you close the window and with the red X then it is closed. If you minimise the window the it should open. So try minimising it instead. Also, when you closed the window and the application still is running then there sometimes is a keyboard shortcut to reopen the window. Remember that you need to be 'focusing' on the application to be able to do keyboard shortcuts that affect that application. To see which application you are  'focusing' on is shown in the upper left corner of the screen.

EDIT: Tried this with the OS X Yosemite built-in mail.app and I was able to reopen the window of the application by pressing the key combination Alt+Cmd+N when I switched to it via Cmd+Tab. This was in tested in Yosemite, remember that it may differ with other versions of Mac OS X.