On occasion, I've had to do some real simple image editing to support technical documentation, design docs, powerpoints, and so on. Here's a technique I used to take a desktop-wide screen shot and highlight one window by fading the rest of the desktop to near-grayscale. You could use this same technique to highlight part of an application screen to draw the viewer's eyes to the part of the picture you want them to pay attention to.
(1) Take a screenshot. Alt-prntscrn works as well as anything else, IMO.
(2) Paste into an image editor. I use PhotoImpact, but virtualy anything should do. You could try Gimp or Paint.net (http://www.eecs.wsu.edu/paint.net/index.html) if you want something free.
(3) Make a copy of the image ("highlight").
(4) You should be able to find a "Hue / Saturation" control in whatever you're using. Use that to dial down the saturation to achieve the effect you want. This can be more subtle than going all the way to greyscale if you want.
(5) Take your "highlight" copy and select the window you want to highlight -- you may be able to use an "edge find" tool, though I seldom have good luck w/ this.
(6) Copy the highlight window and paste into the base that you dimmed earlier.
This should get you pretty close. I don't, btw, know of any tools that make this any more automatic than this, but this shouldn't take more than 1-2 mins per screen shot.