Try this, might do what you want. Be sure you're working on a copy:
      
       1. Create a duplicate layer.

       2. Make sure you're working on the top (duplicate) layer, then
Gaussian Blur the entire image, pretty heavy handed. You want everything to
look airbrushed, just blur it all out.

       3. Create a Layer Mask for the top layer, Hide All. The blurred image
should disappear. Make sure you have your layers window open at this time,
you'll now get a black rectangle next to the image thumbnail. This is your
mask.

       4. Click on the layer mask in that window, then select the airbrush
tool. Also, select white from the color picker (you should have only two
choices, white and black. If not, you're not on the mask layer).

       5. Pick a moderate size but soft-edged brush, and airbrush over the
problem areas. What you're doing now is making a hole (more or less) in the
mask covering the top layer and letting the blurred parts show through.
Thus, in selected areas you're blurring away the rough spots.

       6. If you go too far, switch color to black and touch it up, in
essence closing the hole. Masks are really great things ;-)

       7. If the color doesn't quite look right, or the blurred layer too
dark, tweak it in Curves. Be very subtle.

       8. Now, try this just to control the realism: Change the opacity of
the blurred top layer to let the untouched original layer show through to
some extent. What you'll get is softened rough spots, but you'll have
control over it appearing too altered.

       9. Save this all as a .psd file, which will retain the layers and
masks and allow you to go back and readjust them if needed. Then, flatten
the layers into one and save as your preferred format (.tif or no-
compression .jpg, .tif recommended).

       Should help, and a useful editing tool overall. Or, drop me a line
direct (you know how to reach me) and I'll send along an example file you
can mess with.

       Good luck!

    - Al.

That is just typical overcast sky which gives you those little orphan annie
eyes, black holes where the eye should be.

At least with photoshop you can fix it nicely enough, I would lasso both
eyes with a slight feathering of the selection, copy them to a layer and
give it a levels adjustment, or brightness.    Of course with a couple
hundred photos....  I don't know that you can just make a plug in as you
have to select the area you wish to boost, its not like red eye which is
typically an isolated red color that is peculiar to the type of reflection
it is.  Once you get a routine down, you can make your selections, and then
make your own action to do the layer and curve.

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