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Andy and Alan covered what you need to do. One more thing to keep in mind, check the traffic, you don't want to lose those spot in the SERPS. You might want to consider fixing up the subdomain if it gets you conversions and traffic.

Just want to add one comment. Where people end up in trouble is when they apply the canonical tag too broadly (to non-duplicates). This tends to happen when you have a CMS and one template drives multiple pages. So, let's say that all of your product pages are created by: http://example.com/product.php ...and you just add IDs to that to create a product, like: http://example.com/product.php?id=123 If you add a canonical tag to "product.php" pointing to a single product, you would essentially tell Google to canonicalize every product page on your site to just that one product. This is because that one physical file impacts hundreds of URLs. So, in that case, you would have to make sure the code logic was in place to apply the proper ID.

Hi, As Alex mentioned, as long as you use 301 redirect from old content to new content, that will pass on most of the link juice and Google will know to crawl your new site. However, keep in mind that while doing 301 redirect, you should redirect to content on the new site that is similar or same as content on the old site.  For example: www.example.de's Content A to www.example.com/de's Content A