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.