I use Ksnapshot
, even on my Ubuntu/Gnome machines, because I find it more for my puposes than the Gnome screenshot utility. It's in the repos.
When I want to do what you want, I set Ksnapshot to take a new screenshot after x number of seconds, then open up whatever menu or pop-up I want and keep them open until the timer goes off.
Back in my Windows days, I used to use PRT-SCR (active window) and CRTL-PRT-SCREEN (entire screen) for screenshots. PRT-SCREEN would close any menus or popups when I pressed it, but CTRL-PRT-SCREEN did not.