If you want to check all your backlinks there are Yahoo site explorer and Backlinks Watch, i love this one because it says if your backlinks are non follow or dofollow.
No it doesn't but it does show the important ones and they are all you need to worry about. It doesn't matter if you have 100,000 backlinks if they are all PR0.
I'm seeing links in Yahoo site explorer that do not show up in Google webmaster tools - but perhaps this is just a delay/ lag in how google shows them?
It does show all that it is aware of it seems. Yahoo may show differently. The best way to find pages linked to yours is to use a 3rd party tool.
You can see position for each keyword on webmaster tools but not backlinks. It can help you to improve your ratings and focus on particular keywords.
I suspect they dont alway tell us everything we would like to know/ hear - I see varying results as well
No, webmaster tools only shows a small amount of your link because it is only based on the links within Google database, not on all of the links.