Google doesn’t show all your backlinks from the command, but they index them ALL.
Webmaster Tools will give you a better count from Google.
The PR4 qualification and that a link has to be quality are both myths.
Site Explorer over reports .. show links from images and hot-linked files as well as unlinked URLs contained within content.
If you really want to start looking at your link portfolio use Google, Yahoo, Majestic SEO and possibly LinkScape … do not rely upon a single source