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Thanks Paul, I appreciate you taking the time to answer this.

It's always hard to speak in generalities, but my gut reaction is that Alan's right - if the canonical tags were implemented properly, having your rankings tank from this kind of implementation seems very unlikely. A couple of possibilities: (1) Are your canonical URLs being used in internal links? If you tell Google that one version is canonical but then act as if another version is canonical, it can cause problems. (2) Are you sending any other, conflicting cues, like 301-redirects or Webmaster Tools parameter handling? (3) Is it possible that your canonicalization was too broad? In other words, did you end up de-indexing some product variations that were driving long-tail traffic? For example, let's say you had a product in red, blue and green and you canonicalized them all to the "root" product page. In theory, that might be a good thing, but if people were searching for specifics and you had a lot of long-tail rankings ("buy product in red"), then it could be bad.

It is a custom built ecommerce site in asp.net.