Invert colors of the active window

If you are looking for a method universal for any window, then this must be made available by the window manager. Therefore I'm afraid any non-composite WM will not be able to do that on demand. So maybe you previously did this with Compiz?

A method of inverting colors regardless of WM is doing this per-application - as with xpdf that you mentioned. There are some applications that have such functionality, but usually you won't be able to invert the colors at run-time. For apps like xpdf, you can either have an alternative desktop menu entry (or icon) that runs the app with special parameters, or define those in your .Xdefaults. For xpdf note also the use of paperColor, foreground and background resources.

I found a tool called compton in an answer to a similar question. https://askubuntu.com/questions/134668/how-to-trigger-a-color-inversion-effect-for-one-window