The Backlinks that google webmaster finds. Are they...

[deepsand]

Yes the Backlinks found by the Google WMT have some effects on the linking page's status, but in which way it affects by ..either by ranking point of view in SERP or giving a particular score to the page and then making an aggregate value to the main root domain, that is just an unknown thing. Some say yes it does and some say NO!!

Not unknown at all.

All IBLs, regardless of whether or not they are reported on WMT, affect the target page with respect to PageRank, and the target Domain with respect to Link Profile.

[ozsubasi]

All IBLs, regardless of whether or not they are reported on WMT, affect the target page with respect to PageRank, and the target Domain with respect to Link Profile.

That isn't quite what Google says. Matt Cutts:

"So, for example, the New York Times sent us a sample of literally thousands of links that they were wondering how many of these count because they’d gotten it from some third party or other source of links,” he adds. “And the answer was that basically none of those links had counted. And so it’s a little easy for people to get obsessed by looking at the backlinks of their competitors and saying, ‘oh, they’re doing this bad thing or that bad thing.’ And they might not know the good links. And they might not know that a lot of those links aren’t counted at all". "

[merlot105]

I don't think anyone truly knows the answer to this question. I would venture to guess that, as weegillis states, there are two different engines -- one that computes PR and one that provides you with webmaster details such as backlinks, site queries, and so forth. To be honest with you, as much as I want to believe that PR is so dynamic as to always be "current", I don't think this to be the case. I believe PR is compiled and changed on interval, after a select time period where the engine compiles information about your site. The Webmaster engine is even slower and probably provides you with information from previous compilations. However, I do tend to believe that the Webmaster backlinks provide you with a list of all backlinks that Google has found at that particular point in time - meaning they are not purposely leaving anything out.

[deepsand]

That isn't quite what Google says. Matt Cutts:

"So, for example, the New York Times sent us a sample of literally thousands of links that they were wondering how many of these count because they’d gotten it from some third party or other source of links,” he adds. “And the answer was that basically none of those links had counted. And so it’s a little easy for people to get obsessed by looking at the backlinks of their competitors and saying, ‘oh, they’re doing this bad thing or that bad thing.’ And they might not know the good links. And they might not know that a lot of those links aren’t counted at all". "

The subject of this thread is a narrow one re. links that do vs those that do not appear in WMT.

The matter you raise is of an entirely different nature, that of links deemed to be intended to manipulate PR. If such are detected and discounted, their discounted values are still independent of whether or not they appear in WMT.

[deepsand]

I believe PR is compiled and changed on interval, after a select time period where the engine compiles information about your site. The Webmaster engine is even slower and probably provides you with information from previous compilations. However, I do tend to believe that the Webmaster backlinks provide you with a list of all backlinks that Google has found at that particular point in time - meaning they are not purposely leaving anything out.

Taking things in reverse order, no, Google does not report all IBLs in WMT. Not only is that evidenced by the fact that IBLs displayed there today may vanish tomorrow, but by the fact that Google has expressly stated that it will ot show all, and explained why that is the case.

As for WMT itself, it is not a separate "engine," but simply a reporting tool that drwas from the same set of indices as the public facing search engine.

As for the computing of actual PR, value range 0 to 1, there is no need to wait for while the indexing engine "compiles information about your site," as the only data needed by the PR calculation matrix are page and link counts. Given the relatively low value of the damping factor, there are several mathematical techniques that can be used to recompute an individual page's actual PR with a reasonable accuracy on the fly as new IBLs are discovered.

The only real question is how frequently the entire matrix of PR values is recalculated, and the results re-normalized so that the grand sum of all individual PR values totals 1, as must be the case given that they are probability values of mutually exclusive events. It may be the case that such is done only infrequently, immediately prior and preparatory to the updating of Toolbar PR.

[ozsubasi]

The subject of this thread is a narrow one re. links that do vs those that do not appear in WMT. The matter you raise is of an entirely different nature, that of links deemed to be intended to manipulate PR. If such are detected and discounted, their discounted values are still independent of whether or not they appear in WMT.

The quotation was from a youtube video by Matt Cutts entitled "Will Google provide more link data for all sites?" which makes no mention about links deemed to be intended to manipulate PR, it was part of his answer to a question "In the wake of the demise of Yahoo Site Explorer, does Google Webmaster Tools plan to take up the reigns this product once provided to SEO’s everywhere?"? .
He also said:
"Yahoo Site Explorer, they were giving a lot of links, but they weren’t giving links that Google knew about. And certainly, they don’t know which links Google really trusts. And so I think a lot of people sometimes focus on the low-quality links that a competitor has, and they don’t realize that the vast majority of times, those links aren’t counting".
The question was asked in terms of GWT, and therefore it follows that the answers given refer to links appearing or not appearing in GWT.

When asked to clarify their question, the OP said:

When you look at google webmasters and go to -Links to your site. It lists a bunch of links. My question is, Other programs (SEO spyglass, ext..) may find more links to your website that google webmasters doesn't. The links that webmasters does show you, are those all the links google is aware of and ranks you based off of? What about the links webmasters doesnt show, does google not see those?

and later added:

But the backlinks Google Webmasters finds.... Are those all the backlinks google knows exists (for pagerank and such)?

The OP was asking about the links he saw in other tools (e.g. SEOspyglass) and whether Google saw them, so I believe that the answers given in this video are relevant (perhaps more so as until the demise of YSE, SEOspyglass relied heavily on it as source), and that they clearly indicate that there are many links that Google does not find or count. The New York Times situation was given as an example of this immediately after the explanation regarding YSE.

It seems to me that your statement: "All IBLs, regardless of whether or not they are reported on WMT, affect the target page with respect to PageRank, and the target Domain with respect to Link Profile" is not in agreement with those answers, but please correct me if I have misunderstood.

[deepsand]

That Matt did or did not mention why links may be discounted is immaterial.

The fact remains that what is displayed in WMT is, by intent, a variable subset of all IBLs indexed by Google, such that whether or not a given link is momentarily there displayed is of no consequence. I.e., if Google knows of an IBL, it's appearing for the moment in WMT or not appearing speaks nothing regarding its value.

What links are discovered by crawlers/robots/spiders of other SEs and non-SE applications is of no material relevance to Google related matters.

[ozsubasi]

With respect it was you who said that the first quotation I gave related to PR manipulation, I simply pointed out that it didn't.
Your point that links found by other means are not relevant to Google is what I was illustrating.
Could you please answer my point that whereas you said that all IBLs affect PR, Mr Cutts apparently says they don't all affect it because some are not seen and some are discounted (for whatever reason), as this is relevant to the clarified question?

[deepsand]

To repeat, my statement was within the context of the subject of this thread, which is whether or not the presence or absence in the WMT reported data of an IBL known to Google signals anything regarding its value with respect to either PageRank or the site's Link Profile. The answer to that question is "No."

That Google does not necessarily know of all extant links, or discounts some owing to their being perceived to be efforts at manipulation, is of no material relevance to the subject at hand.