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I totally second and ups on guake, I even find myself hit the f12 key on windows and Macs hoping that my trusty command line will pop down and get out of the way when it loses focus.

as for note taking KeepNotes is my go to application alhtough I had troubles installing it on Mac ( I blame it on too much tinkering GTK with and without MacPorts).

in my windows+linux world I find xrdp invaluable, it is straight forward to install (vnc based) and second only to NX in terms of performance. Since the data is transported over RDP it is much faster than VNC, has some added security, and uses a readily available enterprise friendly client.