Last year I had the pleasure to beta test an absolutely amazing software plug-in suite for After Effects from emotion3D, a company based in Vienna, called Stereoscopic Suite X3.
The software can automate geometry correction, color matching and also offers powerful depth grading and QC reporting functionality. It's approx. $10,000 - so not exactly in-expensive, but I have not seen anything with this level of power and accuracy for 3D other than SGO's Mistika - which is a six-figure DI system. They are currently working on porting the plug-ins to NUKE.
The software can create per-frame, full-resolution disparity maps which can facilitate accurate rotoscoping (roto one eye - disparity re-calculates the roto shape for the other eye) and allows depth grading and re-projecting so that you have much more control than just using HIT (horizontal image translation).
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