For some time now when I open a Nautilus window, no icon appears in the Launcher, and when Alt-Tabing, the Nautilus windows are ignored too.
I'm using Ubuntu 16.04 with unity.
EDIT: I'm no longer experiencing this problem. It went away roughly at the time I uninstalled Dolphin, may that's what was causing it.
This seems to be a bug in 16.04 see #1578792 and 1572348
As a workaround till this issue is fixed you need to pin Nautilus to the Launcher.
Make sure you leave the nautilus icon on the Launcher (no pressing Unlock from Launcher) as otherwise the icon will disappear again.