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For a while I used vimwiki in a drop-down term: guake and yakuake have this as a primary feature, good for gnome/KDE, but if you're using a tiling WM you can use termdrop on most terminal emulators.

good point, I should try this

You could run it in tmux then set the background and or frame of the window to something that stands out.

I used to use a Vim GUI (Macvim) just for notes, terminal for everything else.

I use terminator, one window, tabs, and vimwiki is always my first tab.