Accurate Backlink checking

Hi All,

Since starting a site I've noticed that yahoo site explorer doesnt actually show all links. Google webmaster tools also seem to show different ones.

My question is this: how do you accurately assess competition if you cannot find out how many backlinks sites have?

I realise there may not be an answer but, just wondering if there is something I am missing as I'm still learning. I know I could use something like marketsamarui but, at this (learning) stage, I'd rather learn how to do this stuff manually.

Also, I know that supposedly google doesnt give any 'juice' to nofollow links. So is it right to think if a site has hundreds of links back to it but they are predominantly nofollow, then these dont count? A site I'm looking at has lots of links from high PR domains but they are all nofollow. They currently rank higher than me (I'm not even a month old yet), so just wondering if I should be able to overtake them since most (not all) of my links will be dofollow.

Is this thinking flawed?

Thanks so much