From my experience if you have created backlinks using some software of anything like that such links usually not get indexed in google as well as if somehow they get indexed ultimately these backlinks are removed after some time..don't know about others But I prefer to do all my backlinking 101% manually..
I build my web2.0's and facebook/youtube/twitter etc manually cause I want them to stick for some time, also I make high relevant blog comments on high PR pages which isn't possible to automate. All the rest I do automatically (comments,directorys,pressreleases,socialbookmarking,articles,profiles)
of course manually is the best and my website page rank has been increased with this method . Please check here : http://indexhttp.com/2011/11/20/special-seo-service/ + http://www.1buy.info/top_backlinks.html
I remember I created a single link on Wordpress forums about my footer decoder (its not hosted now). that link brought 100s of unique traffic daily. how did I find it? I searched Google for proper place where people might be talking about things that I have now. so why not share there. They will be glad. It'll be relevant.