We want to see landing pages that came from organic searches, so first we need to add to this dataset the parameter “Medium” which is how Analytics identifies channels. To do this, use the drop down above the table of data and locate the option for “Medium”. The table below should refresh and now you will have a second column of data showing the channel for each landing page.

Another tip you can use is just reach out to the prior agency and say something like the following: “We realise you were using link networks for our website which has resulted in a Google penalty and loss in business. Can you please remove my website from any link network you have built?”. If the prior agency is decent, they will remove the links from the network.
Traffic data is a great way to take the temperature of your website and marketing initiatives. When you are writing and promoting blog content on a regular basis, you can use traffic data to track results and correlate these efforts to actual ROI. Be sure to look at traffic numbers over long-term intervals to see trends and report on improvement over time.  
The online space has definitely become extremely competitive. New businesses, platforms, and complimentary services are entering the market almost every day. In fact, nowadays you can even set up an online store in just five minutes, but to sustain it as a profitable e-commerce business requires significant amounts of time and resources, plus a great amount of business experience and marketing knowledge.
Another point which you did mention (between the lines: "and updating your backlinks to point to HTTPS URLs") but I actually didn't realize enough is that updating backlinks when your site switches from http to https is very important. Redirecting all http traffic to the https version of your site from the server (301) is necessary, but doesn't solve losing referral data. Only updating backlinks, especially those on httpS-sites, does. I'd like to emphasize that!
Incidentally, according to a June 2013 study by Chitika, 9 out of 10 searchers don't go beyond Google's first page of organic search results, a claim often cited by the search engine optimization (SEO) industry to justify optimizing websites for organic search. Organic SEO describes the use of certain strategies or tools to elevate a website's content in the "free" search results.

The top five leaders in paid traffic (Google Adwords) are the same companies that lead in search, with Amazon again on top. Leading retailers don’t want to put all their eggs in one basket, and they are willing to invest heavily in pay-per-click campaigns. Clearly, PPC has worked for them because we see four out of the top five spenders are the leaders in annual sales numbers.
Note the penultimate processing step (previous campaign within timeout), which has a significant impact on the direct channel. Consider a user who discovers your site via organic search, then returns via direct a week later. Both sessions would be attributed to organic search. In fact, campaign data persists for up to six months by default. The key point here is that Google Analytics is already trying to minimize the impact of direct traffic for you.
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Wow, great post, Brankica!!! I've used Flickr in the past and while I haven't gotten much traffic from it, I've gotten a ton of backlinks. Like there's this one photo in particular that I tagged as "SEO" and included a link in the description back to the blog post I used the photo in. I guess there are lots of autoblogs that scrape stuff like SEO-related images, and since they scrape the description, too, I get lots of automatic backlinks. Sure, they're crappy backlinks, but still backlinks :)
Another tip you can use is just reach out to the prior agency and say something like the following: “We realise you were using link networks for our website which has resulted in a Google penalty and loss in business. Can you please remove my website from any link network you have built?”. If the prior agency is decent, they will remove the links from the network.

Secure (https) to non-secure sites (http): Since Google began emphasizing the importance of having a secure site, more websites are securely hosted, as indicated by the “https” in their URLs. Per the security protocol, however, any traffic going from a secure site to a non-secure site will not pass referral information. For this issue, you can correct by updating your site to be secure through a third-party SSL certificate.
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