A couple of months back I launched Data Moving Tool, an application to Extract, Transform and Load data to and from any data source (database, flat files, etc).
In an effort to boost my online presence, I placed my application on download.cnet.com. I was pretty happy with this until I discovered that a lot of other less reputable download websites had "high jacked" my software by publishing it too (or just some dead junk link about it). To name only a few: download.famouswhy.com, softsea.com, creativx.net, wareseeker.com, etc.
Searching for "data moving tool" on Google used to bring back my website in 1st or 2nd position on the first result page. Now thanks to this my website buried down on page 4!
I'm wondering if anybody had a similar experience and found a way to overcome it (i.e. get back on top of the search results or "unregister" from all these download websites).
You need to work on link building for your website in order to outrank them.
These download sites have been around longer than any newer websites. Hence they have more authority and back links to support them. So if your product is used as a keyword in the search engine, then the search engine has no other way to tell if this keyword belongs to you or the download sites.
The only way to associate this keyword with your site is to build more reputation. One of the ways to build more reputation is more content on your own site and backlinks to your site with this keyword or associated keywords.
Slowly the search engines will recognize this as time goes. For now the download sites have an edge and may be you think of ways to direct traffic from these download sites to your site. So you don't loose traffic.
The sites that have hijacked your software by publishing as well are most likely using dodgy link building techniques. If you want to get back and get to the top again, I would suggest doing some link building and getting some authoritative backlinks to your website from similar relevant websites.
I had a look on the google keywords tool and "data moving tool" gets around 140 searches a month. So I wouldn't worry too much about ranking for those keywords.
"data migration tools" gets 3600 searches a month, you might be better doing some on-page and off-page seo for those terms.