Where are (partial) screenshot stored or how to specifiy location?

As I know holding Ctrl copies the screenshot to the clipboard and you need to paste it in an application to save it.

You can check the shortcut keys in Keyboard Settings.

I played around some more and found that using Alt-Fn-PrtScn will copy the window only and then give me the option of where to save.

2014 - Update

PrtScn - Capture the entire screen (all windows) and ask where to save
Alt PrtScn - Capture the currently focused window and ask where to save
Shift PrtScn - Select specific area for capture and ask where to save

Shift+PrtScn is a better way, as you will be prompted for where to save the screenshot (and by what filename).