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There have been some reports of people running into trouble from mass-301s, and a mass-404 might look odd to Google, but I suspect any issues would be temporary. You're not going to be penalized for removing your own content, but there could be crawl consequences and you will definitely cut off the link-juice. So, whether or not it's a Capital-P "Penalty", you may lose ranking and traffic.

If this is preventative, and you don't currently have a problem, I'd suggest taking it in stages. 404 or META NOINDEX the thinnest content, layer by layer. If it has any relevance, 301 it to something appropriate. That way, you can also gauge the traffic loss from any links you're cutting. I'd hesitate to do this all at once, unless I knew I had a problem.

I think Istvan is absolutely right. You need to canonicalize somehow - it could either be the canonical tag, or you could capture the tracking ID into a cookie and then 301-redirect to the canonical version.

This looks even worse than a typical tracking parameter situation, where it would just be tacked on at the end. It looks like the entire URL structure is changing. Honestly, any CMS that requires this is pretty outdated, IMO. As a former developer, I don't completely buy your developers' story. Doing it the right way may be a lot harder - it may not even be cost-effective - but it's far from impossible. If this structure is weird enough, the canonical or 301 could end up being band-aids.

Sorry, the thread was getting a bit nested, so I'm breaking out this response, even though it relates to a couple of replies. Although it is tough to tell without specifics, I suspect that you do need to canonicalize these somehow. Geo-pages that only differ by a keyword or two didn't fare well in the Panda updates, and Google is starting to see them as "thin" content. I do actually think the canonical tag is preferable to a 301 here (at least from my understanding of the problem). As Aran said, the 301 will remove the pages for visitors as well, and they may have some value.

While they're technically not 100% duplicates, Google is pretty liberal with their interpretation of the canonical tag in practice (in fact, I'd say they're actual interpretation is much more liberal than their stated interpretation). If the pages really have no search value, you could META NOINDEX them - it's unlikely that they're being linked to.

I'm afraid I have to generally agree with Dejan SEO. First off, the evidence that .edu and .gov links are really valued higher (at least over the last couple of years) is limited at best. SEOmoz did a correlation analysis in 2010 that suggested .gov links only slightly outperformed .com, and .edu under-performed .com -

http://www.seomoz.org/blog/google-vs-bing-correlation-analysis-of-ranking-elements

Part of that may be due to the fact that higher education sites have been relentlessly spammed. It's just too easy to set up a profile on a deep page and get a cheap .edu link. That's the core problem, too. In general, a .gov or .edu site may have more trust or authority than the average .com (although I can't even prove that). That doesn't mean, though, that EVERY link on a .edu is worth more than EVERY link on a .com. That's a gross oversimplification that ignores the dozens of factors that define a link's value. See Rand's post here:

http://www.seomoz.org/blog/10-illustrations-on-search-engines-valuation-of-links

If you have a deep link on a .edu site on a page with no inbound links that links out to 400 sites, all of which are irrelevant and spammy, that link will be crap. It doesn't matter that it's on a .edu. That page may not even be indexed. Chasing .edu or .gov links ignores a lot of other factors.

Is suspect the international links are treated much like their .com equivalents. If your site operates in the US and is in English, and you get a .edu.tw (or .com.tw) link from a Taiwanese site written in Mandarin Chinese, that link is going to be low-value in the vast majority of cases.

I hate to advocate full-scale blocking, but if you really took a hit, and you know the timeline coincided with the new content, it is possible. It might be better to scale back and re-roll out new content in chunks.

One warning - if this is a regular filter (you added a bunch of duplicates), Google should start re-ranking content as soon as the blocking kicks in (this may take weeks, not days). If this was Panda-related or more severe, though, it could take a month or more to see an impact. Not to be the bearer of bad news, but don't Robots.txt block the pages for 2 days, decide it didn't work, and unblock them.

A slightly less extreme approach would be to META NOINDEX all of the pages. That way, you could start to selectively lift the NOINDEX on content piece by piece. If you Robots.txt block all the new directories, it's going to be hard to re-introduce the content. You'll end up releasing the block all at once and potentially just having the same problem again.

Given the current state of local, I tend to agree with Robert. Those local results seem to dominate in some cases and they're a powerful draw for search visitors. I should add, though, that it's possible to be in the 7-pack AND organic with blended results - sometimes, Google actually counts a listing as both.

I'd say it also depends a lot on the nature of your business. Some queries/industries are naturally local-oriented, and you have to compete in that space. For some queries, local won't matter at all. If your business is naturally local, though, and many queries produce 7-packs or blended results, that's where you have to compete.

Usually, Google is pretty good about ignoring those, but if the links are crawlable via the Google Shopping engine, it could be a problem. One big problem - you have canonical tags in place, but they dynamically set to whatever version the person landed on. So, the canonical tag for the Google Shopping version reads:

rel="canonical" href="http://elettrodomestici.yeppon.it/cura-corpo/tagliacapelli/remington-tagliacapelli-funzionamento-rete-ricaricabile-lame-in-acciaio-inox-hc5150-garanzia/?utm_source=google_shopping&utm_medium=web&utm_content=Elettrodomestici+e+Clima+%3E+Cura+del+corpo+%3E+Tagliacapelli&utm_campaign=google_shopping" />

That should never be the case - it should be set to the actual canonical version (without the parameters after the "?"). By setting it this way, you're reinforcing the problem. If you can't fix the canonical tag, then remove it - having it this way is worse than not having it.

Fixing the canonical is your best solution, but if that's not possible, then remove it and use Google Webmaster Tools parameter handling to block the utm_source parameter. It's not the ideal solution, but it should do the trick.