Google Webmaster Tools does show all backlinks to your site. However, the links that showing are coming from "Google Own Ways of Links Judged" so you should not compare to Yahoo Siteeexplorer and question why different. Two of them have a completely different on links judged and quality defined.
Google also shows some nofollow backlinks in my webmaster tools. So I assume those links are still from high quality to google even they are tagged with the nofollow tag.
Where have you been so far? If you don't have an account with yahoo so get going NOW! LOL Yahoo Site Explorer shows you the true amount of inbound links to your site in compare to Big G's webmaster tools. Even Bing's webmaster tools handle inbound links different than Google does. It's really interesting to compare all 3 of them. I love Yahoooooo, because it shows me the efforts I made in link building. Google frustrates me and Bing, well Bing is ok. LOL
MegaDave, Google doesn't show all inbound links to web site. Google shows almost all inbound links in it's webmaster tools. To see change it takes about 3 - 4 months to see new inbound links.
google webmaster show all the backlink that you have (Even if it's dofollow or not) so if it shows a lot of backlink, don't happy yet because they won't use that to increse your PR. And why i said so? Because i have 2 website with google, 1 with overs 8000 back link and got PR 0 Another site with over 800 back link but I have some quality Pr4 and 5 so it got PR 4 This is my own experience, if you have another exp, please do share it here thank you
SO does Google actually 'log' links marked nofollow and just not 'follow' them? Not sure I understand.
If you ask Matt Cutt about it then he will clearly say that webmaster tool is set to show all the do-follow & no-follow links. Still if you consider my personal experience then Webmaster tool do not show all the links and they take months to collect links.
Yes Google webmaster tools does not show all the links. Though it updates the data regularly. But it does not update the incoming links links regularly. I think it shows the result once in a month or more. And above that it does not show all the incoming links like yahoo. It shows only the do follow links..
google shows it difference .it says it does not follow no follow links but when I see my external link table it shows links from mixx which are no follow