Removing from dock when quitting
I found an answer here: https://superuser.com/questions/53935/getting-mac-os-x-applications-to-close-after-last-window-closed

Essentially, there's a program called RedQuits that automatically quits application when you close the last window.

BUT, it does no work for Yosemite. So still no dice.

The thing about applications not closing when hiting Cmd-Q was probably me misremembering things, because I couldn't find back any application doing that.