In what way do you feel that the Webmaster Tools change is a factor for SEO? I've always understood that Google adds links continually but only makes them visible in WMT once in a while. Yes they may show more links in WMT than in the link: operator, but it's still partial and still a delayed report.
Last year i managed to get myself out of the -30 penalty bin for one site, and i have been studying the WMT internal links ever since.
Given the fact i run various sites some more popular than others i have a very strong case to suggest the more internal links you have the the more trafic you are likely to get so long as the 'on page' is done correctly.
I have also noted that in your WMT all links in there will have a white bar or PR.
A few of my pages that has always been a pr2 went to grey a couple years back and the other day it appered on the internal links and then bang it went back to PR2.
If you have suffered a penalty you may also that you have a loss of links in there too.
I've observed the same. I have also noticed an improvement in ranking on some pages immediately following their addition to the internal and external links list in WMT.
Sometimes there can be a very long wait (many months) for Google to update the links pages.
I think you're seeing the effect rather than the cause here, or maybe we're just not using the same terminology. Naturally, when a page is no longer gray-barred (for whatever reason) it will have a chance to rank. It could be that WMT doesn't report links to gray-barred pages and once a page breaks back into normal PR status it starts to appear in the WMT reports.
It seems to me that the better question is what causes a page to stop being gray-barred. The only thing I've ever spotted that works is a good link from an external (unrelated?) site, and I'm not at all sure about that.
What I mean't was that there was an immediate improvement in the ranking of the page in the SERP's. But yes, I guess that naturally flows on from an improvement in PR status that comes from aquiring a good backlink from a page on an external site that is not grey-barred.
But why does it have to take many days, weeks or months since acquiring the backlink? - It appears to me that a delay in updating the reports in WMT will also result in a delay in improvements seen in the SERP's.
Does Google update this section in WMT more frequently for some sites than others?
WMT is a very delayed reporting tool, infrequently updated (though more frequently than TBPR).
Ranking is iteratively calculted several times a DAY, updated in real time.
Its like saying that we in the UK have only just gone into recession. It was only officially announced this week (after statistics show 2 Qs negative growth), but the EFFECTS of the recession have been felt for months. Just because WMT is only showing the data now doesn't mean the SERPs have not taken it into account for a while.
BTW, the strength of a link matures over time. Full value might take between 6 to 24 months to show.
I disagree with the external link as i have had plenty to 1 particular page that did not stop it being grey bar for 2 years.
I seem to get updates at the start and end of each month.
i have being trying different things to see how to get more links into the WMT links, the only real thing is to make sure a page is completely unique.
Theres some funny stuff going on with google toolbar at the mo!