Here's a quick photoshop fix I figured out because I wanted clouds in the reflection image I was using in my scene.
1. First I start with the original image. blue sky.jpg
2. Then I stretched thesky so I would have more sky in the reflection. This can be done a number of ways. I just added the color, then used the healing tool to smooth it out. blue sky-taller.jpg
3. Now find a sky image that has some good contrast such as this one that is offered for free by 3dallusions.com 3D Allusions - ReMOSitory sky_020.jpg
4. Now, to copy only the clouds into your image, in the sky image, push ctrl+L (levels). Now if you click the bottom left ink dropper (set black point) then click on the darker areas of your sky image. You will notice the blue in the sky turns black. If some areas are still pretty blue, click one more time in a blue area with the black dropper. Your result should look something like this. sky_020black.jpg
5. Now push ctrl+a (to select all) then ctrl+c (to copy), then in the channels palette create a new channel. Now push ctrl+v (to paste the black sky as a channel).
6. Now on the bottom of the channels palette, click the dotted circle which is the "load channel as selection" button. You will notice the imagenow has some areas selected. It may look like it isn't selecting everything you want it to, but it is. Click back on RGB channel, then drag the selection with the move tool on to your original image.
7. Adjust the whiteness in the hue and saturation adjuster (ctrl+u). Adjust the size of the clouds (ctrl+t). If you need the clouds stronger or more opaque, then duplicate the layer. sky-fixed.jpg
This should work on pretty much any sky.
Please note, the imags I attached to this tutorial are downsized for the forum standards and not the original image size. You will want to find your own images to use in your renderings