We are in a very competitive industry and in late April 2004 we launched a new site and started on a small link-building campaign (didn't want to do too much at once), but have not yet seen any results despite having what we think is a site that should be ranking much higher than it is. When we launched this new site we also switched domain names, using a 301 redirect to the new domain from my old domain.
Since we have not seen the results that we were expecting we have also began several experiments to try and pinpoint the reasoning. One thought was that perhaps our IP had been flagged as "bad" due to some "borderline spammy" things we had tried years ago.
To test this theory we recently launched a brand new site with a brand new domain name (and IP) and exactly copied one of our pages to this new domain/IP. After 2 weeks the "experiment" site ranks as #297 for a three word keyphrase and has only 2 IBLs (Google actually reports no IBLs using link:www.experimentdomain.com, but I put 2 links, both on un-related sites with a PR of 6 - just to get Google to discover the new site.) Both the home page and the page targeted by the three word keyphrase have a Toolbar PR of 0.
The site launched in April ranks as #298 for the exact same three word keyphrase. This site has many IBLs and is listed in many top directories including Yahoo! The home page has a Toolbar PR 5 and the page targeted by the three word keyphrase has a Toolbar PR of 4.
We interpret this to mean that Google is currently ranking both sites based purely upon "on page" characteristics and is not yet "giving us credit" for any of the inbound links, either new ones or ones that point to our old domain (that is now 301 redirected to the new domain).
Does this theory make any sense? It seems to be similar to the March Filter but we're also open to the idea that we just suck. :)