Have you ever tried creating rss feeds for your backlinks? For Example, I keep the direct urls to all my backlinks. Once I have implemented and made sure they are actually "dofollow" I go ahead and add a rss feed by using a script. Once the RSS feed creates a link around those backlinks, I go to w3c to make sure they are properly RSS'd. After that's done, I ahead over to pingomatic and add my created link there that points to all my backlinks. Within 30-45 minutes, Those backlinks are more or less indexed. This is my process and if you do the same, you should never have any problems with Google indexing your backlinks. Hope I helped you out. It's a bit complex at first but process takes you no more than 2 minutes to implement after your ready to create the rss feed.
Haha. Yeah, you have to make sure you keep up to date with Google. I would say its nothing to worry about, just keep doing what your doing and it will all come together. Make sure you don't implement any fast backlinks all in one day and then stop doing them. Keep building those links on a consistent basis.
If you want to know what google has indexed, look in your google webmaster tools. Yahoo will show nofollow links in their search query, you have to take that into consideration when trying to compare the two.
one thing to take into consideration is time frame, if you do links to quick google takes very long to index. because of control of PPC. Before you can rank very fast for Bing and now it has shifted back to yahoo being quickest and bing lost its speed to index links. It is all about control.
It's not quite clear whether you chedked your backlinks with Google Search's link:mysite.com expression or you have used Google Webmaster Tools. If you used Google search, then it is true that generally this method always shows much less backlinks than Yahoo!, no matter how valuable your backlinks are. If you checked it with Webmaster Tools, then I must say sometimes this tool does not show any backlinks for a while, even if your links are older and coming from sites from good reputation.
Canonical issues: If you are using dynamic content with SE friendly urls, these non-friendly urls are still accessible by search engines. You need to tell to the search engines witch page is one you prefer to be indexed. That happens with canonical link <link rel="canonical" href="URL_TO_THE_SE_FRIENDLY_PAGE" />. That has to be found from the inside the head-tags. At least with PHP, these can be build with the database information you are using when building these friendly urls in the first place. Google it and you will find the Google webmasters blog describing this method more clearly. Internal duplication: Is you site accessible through www and with out it. Choose one of them. In Apache server this is done with the .htaccess file. Poor linking structure: How I understand it, you should have planed how the link reputation will spread through your site. Where to use rel=nofollow and where not. For example, does your TOS page have to be indexed by the search engines? Guess not, so the nofollow might be an option there. Also, how is your site navigation handled? Do you use heavy JavaScript on them? SE can't follow these links and the link reputation is very poorly spread. How about other internal links...like related articles? These are good way to get the "Google love" served to every page you want. Hope this helps even a bit...
Thank you! A lot of useful info. I'll try to use it as much possible. Btw, if i rank on 1. page on Yahoo, can I expect that to happen in Google after a longer period of time? Or they are completely different?