Working with stereo images is difficult, because there isn't a single good tool to manage everything for you. Fortunately, there are a couple of good tools, and a relatively simple workflow to follow!
Tools:
Stereo Photo Maker (SPM) - free
Picasa - free (Can be replaced with your favourite photo editor)
Format:
Most (all?) photo management software can't understand MPO or JPS files. Juggling pairs of images is a nuisance; you might lose, rename, or edit only one of a pair. I recommend a single-image, side-by-side format. I keep mine crossed, not parallel, because I prefer it, but many prefer the other way around.
(example side-by-side crossed-stereo image)
Overview:
Convert to side-by-side images, aligning as you go in SPM (batch job)
Tweak stereo window, rotate and crop, in SPM - these are now your permanent files for storage.
Manage contrast and colours in Picasa
The reason for this workflow, is that you do the most essential editing first - there's no reason to keep non-aligned images, or images with a poor stereo window. When you've done this editing, you keep those files and you can always revisit how Picasa treats them, because Picasa isn't an image editor (jump to the section on Picasa below if you don't understand this).
Below, I have more tips on using the software for the different stages, but if you're familiar with the tools, then the above is the entirety of my recommendation.
I have a Fujifilm W3. Unfortunately, it's a pretty bad camera (there isn't a better one currently available), but it does synchronised stereo in a single relatively small device and this more than makes up for its shortcomings. The native format is .MPO files (multiple-picture-object).
In Windows, you can at least get file-system previews of the images, but I prefer side-by-side anyway (in case that link dies, here, I needed to run run the reset script first but it worked for me in XP, Vista, and Win7).
The first step is to convert the MPO files to side-by-side images. This runs as a batch job so you only need to press "go", and you can walk away and make a cup of tea while it processes. It's going to take a while because we're going to align as we go - even images from a stereo camera need alignment because they're often slightly off in terms of vertical position and rotation. Running alignment now means that you don't need to bother with it later in the manual phases, so it saves a lot of time.
Even if your starting format is already side by side images, you can do this step to get your images aligned.
Fire-up SPM and choose "Multi-Conversion..."
The screen that you get is too complex! As a quick guide:
Choose input images - top, red
Select the output format - middle, red
Choose an output folder - bottom, red
Set AutoAlignment - upper middle, blue
Set Crop (squares off after rotation) - lower left blue
For crossed images (not parallel) - lower right blue
Press Convert! - bottom right corner, red
Point of order: To keep your photo's EXIF data (time taken, exposure setting, etc), you "Add Thumbnail" via the "Output File Setting".
As one final point of recommendation, press the "Auto alignment Setting" button (upper middle, blue in the image above), and get the window shown.
Choose "no adjustment of the stereo window", otherwise SPM will attempt to guess the correct depth for the image for you. No automatic software can do this well, and you might the lose sides of the image unnecessarily if the guessed depth is wrong! You really have to adjust it manually later anyway, so best to leave it not-adjusted:
Since the alignment already happened in the batch phase, your images should now be ready to go. SPM assumes that a single loaded image is actually a wide stereo pair.
All you need to do is:
Rotate the the image to straighten it
Crop and adjust the stereo window (depth)
You can also colour-correct the images to match if necessary (the histogram of the right image is always altered to match the left one). I've never yet found colour-correction to be necessary for photos from my W3, but sometimes for pairs of single photos taken with a normal camera. The colour matching feature can introduce some artefacts if the images are too different. A workaround is:
Save separate left and right images
"I Feel Lucky" in Picasa and re-export (this does histogram equalisation, which you could also do in other image processing software such as Photoshop or Paint Shop Pro)
Back to SPM and then colour-match
The histogram equalisation balances out the images, so that they should have similar content. When you colour-match in SPM, there should be less to change and fewer artefacts introduced.
In the sample image above, you can see the book cover leaning forwards, and the Holmes Scope looks like it's hanging down instead of being mounted.
In the sample image above, everything is skewed the other way, the book is at an odd angle.
Absolutely vital and not artistically-negotiable for a stereo image, is that nothing can stick out of the image at the edges. This is called a "window violation". It should be called a "window-frame violation", because stuff can stick out of the middle of the image as much as you like - in fact it's good when it does - but not at the edges. Why? Try it once and you'll see how uncomfortable it is to the eyes.
As a general rule it's also a good idea for it to be as close to the window as possible - there's no point in your whole image hanging in the distance.
In the image below the closest thing to the camera is the card plate at the lower left corner - circled in yellow. Because it's at the edge of the image it can not stick out of the window, it needs to be inside the window ("behind the screen" if you like).
In the example above, the front edge of the Holmes scope is about at the screen depth as you can see. This is a shame because as it's the focal point of the image, we'd like it to stick out!
There is something that you can do about this: You can crop the image.
In that picture, the book is still an object of interest in the background, but there's no need to have the card in the lower left corner in-frame. We can crop the image then, and bring everything forwards:
As you can see in the image above, the card at the bottom left is still the limit of how much we can zoom in because it's the closest part of the edge of the image, but the visible portion is further back than in the other image above, so we can bring the image forward. Now that we have zoomed in we can see that left edge of the Holmes Scope is now sticking out of the window - hooray!
The other thing that you can achieve with cropping is reducing the overall depth of the image. The limit to comfortable stereo depth is about 1/30th of the image width. This rule-of-thumb is widely known and a pretty good guide.
In the first image above, you can see from the anaglyph ghosting at the top left that the stereo separation is quite large - just above 1/30th of the image width. I measured it, it's 28 pixels out of 800, so just over (800/30 ~= 27). Although the second image is smaller meaning that the image width is smaller and hence the acceptable separation is smaller, we've been able to bring the scope forwards, and you can see from the ghosting in the book that the separation is less. The book is 24 pixels out of 800, just below 1/30th. This is a pretty small change, but it's an example of how it can help to crop.
The furthest thing from the camera in both images is the map drawn on the back of the display case. It's about the same in both images - 32 pixels, which is above the rule-of-thumb 1/30th limit, but it's not a focal part of the image and it doesn't have high contrast so I can get away with it here.
There's an important thing that you need to know about Picasa:
Picasa never edits your files
What Picasa does, is record a set of changes to be applied to your images before viewing/export. You can edit and tweak a photo as much as you like in Picasa, your original is never modified, recoded, or degraded. You can export an image with all your tweaks, at any resolution or quality, but that still doesn't edit your original.
This is why Picasa is the last step of the workflow - it doesn't edit the files in any way.
I once read a complaint that Picasa doesn't have a resize function, which is exactly an example of missing the point - there's no resize because you're not editing your file! You can however, export at any resolution that you like.
Okay, point made, so how to use it?
When you install Picasa, it asks you where you keep your images. Once you tell it, all you need to do is add more images to that folder and Picasa will automagically find them. In Windows, the default "My Pictures" location is a pretty sensible location. I keep a "My Photos" folder separate to "My Pictures" - helps to separate my photos from funny pictures online and comics that I've saved.
Side note: With a Google account such as gmail, you get a free 1Gb of online storage space at picasaweb. With this, you just select some photos in Picasa and press "upload", which is how I have shared all of the albums linked on this site.
Back to editing: Here's a stereo photo that I took of some wine-glasses at a dinner. It's already been aligned and cropped (I removed one wine-glass from the left, allowing me to get the existing ones to poke out of the window a little):
The basic tools offered by Picasa are shown at the left. For a stereo image pair, you can't crop or straighten obviously - Picasa doesn't know that you have an image pair and the results will be wrong. You can however, use the colour and contrast features. "Auto Contrast" does a histogram equalisation of the image brightness, and "Auto Colour" does the same for the image chroma. "I'm Feeling Lucky" does this for both. Histogram Equalisation has the effect of taking the brightest thing in the image and making it white, and taking the darkest thing and making it black, and stretching out everything in between. I press "I'm Feeling Lucky"...As you can see, the image has a little more contrast, and a little more colour, and the equalisation has brought the colours in-line with each other to make the table cloth a little whiter. The green oil in the little bowl especially has come out a little.
Next, we can go to the image tuning, as shown. "Fill Light" brightens the whole image evenly. "Highlights" takes the bright areas and makes them brighter, leaving dark areas alone. For outdoors photos taken on a cloudy day, it makes it look like a sunnier by making light objects look like they're reflecting more light. "Shadows" makes dark areas darker, and is especially useful for taking grainy dark areas and making them look smoother simply by darkening out the grain. Finally, "Colour Temperature" tweaks the whole image between blue at the left and red at the right. A slight "warming" of the image is often pleasant. For the image below, I've used a slight move to the left for all the sliders, meaning that the image is a little brighter, has a little more contrast, and feels a little warmer:
The last thing to do, is look at the effects. Mostly, these are special things that you can try if you like, but not really applicable to photo editing... Except one, Saturation. For the photo below, I've increased the saturation just a little (too much and a photo will look bad and cartoon-ey - the adjustment below is actually less than the recommended amount when you press the button). As with "Fill Light", "Highlights" and "Shadows", this can help some images in small amounts, but will look bad if used excessively. You can see the results below. It's subtle, but the pink wine in the glasses stands out just a little more.
There is one more tweak to do. Look back at the "Tuning" tab, and notice that I skipped past the "Neutral Colour Picker". What this does is lets you pick a shade of clean white or pure grey, and tweaks the colours such that they become un-coloured. If I do this for a piece of the white table-cloth, I get a dramatic difference, as below:
Ta-daaa!
Although it looks blue-ish compared to the image above, you'll see that on its own it's actually a clean white while the images above are skewed. Once the tablecloth is a neutral colour, the pink wine stands out nicely and the green oil too. I'm not sure, but I think that this cancels out the colour-temperature adjustment.
I hope that this has been helpful!