As a software developer company we do websites to our customers. In these websites we always put a link linking back to our site.
However, we did today a Google search (link:http://example.com) to see which sites were linking back at us, and the result was empty.
Can someone explain why these backlinks on our customers websites are being ignored by Google?
Using the link: operator is not an accurate or official way to find out what links you have to your website. Google omits links on purpose to prevent SEO analysis of other websites you do not control.
To get an accurate report of your incoming links you need a Google Webmaster Tools account. Under Search Traffic > Incoming Links you will see what links Google has found for your site.
As John Conde pointed out, the link: method is ridiculously inaccurate.
However, I'd also like to point out that Google Webmaster Tools isn't fully accurate either and that it can take a noticeable amount of time before links begin to display (Google have admitted this themselves). If you read this FAQ, you'll see:
Q: I know I have [one / several / dozens of ] links that Webmaster Tools isn't showing. What gives? Although the link reports in Webmaster Tools are more comprehensive than doing a [link:example.com] query in Google search, they may not include 100% of all links that you know about. This is normal and should not be cause for alarm. Webmaster Tools does not always show 100% of the links that Google knows about, so just because a particular link doesn't appear in Webmaster Tools doesn't mean that Google doesn't know about that link, or that your site isn't "getting credit" for that link.
Note that the link report in Webmaster Tools only shows whether a site is linking to yours; it doesn't show which links are most significant, and it can include links that are nofollowed or that don't pass PageRank.
If you're desperate for more accuracy, then you might want to look at some of the paid services that are out there: Ahrefs is one service that gets a lot of credit.
In addition to Google Webmaster Tools, Majestic Seo has a horde of bots that people volunteer to run. It crawls quite frequently so has a rather accurate view of your backlinks schema. There is also Open Site Explorer, but that seems to index less. If you want a neat way to check literal source for your links, NerdyData has a decent pool, although not as much as suggestions above.
Other than that, assuming you use Cpanel, an accurate way to find backlinks people are actually clicking through is using the Awstats module for the domain(s). Log into Cpanel then find the link for "Awstats". If its not there, ask your host to enable stats for your account, or if you have VPS, get into WHM and change the package/features for the account. When in Awstats, look on the sidebar for "Referring Sites".
Between the 5, this should give a decent scope of backlinks.
A reason why your backlinks may be ignored: If you find that Google no longer cares about your footer backlinks, well thats because you're more or less spamming your link. If your dev company has nothing to do "content-wise" with your clients (a la LSI), this would fall under the umbrella of "poor quality backlinks". Little by little Google may start to de-rank you because of this circa 2003 tactic. Also, no client wants your tags all over their site, especially if you don't pay them, so removing them is win win.
So what are proper backlinks in an LSI era? Well stick to sites within your keyword schema/scope. Forums, comments, tutorials, guest blogging, open source projects, etc are all great places to legitimately build a backlink pool that will actually work. Our favorite is the forum approach - simply answering other peoples questions, guessing what would be a hot guide, and including your backlink in signature. Google likes these more because its relevant content<->content.
