With the recent Google Webmaster Tools security bug, I thought a deep dive into what GWT has to offer SEOs might be prudent since many SEOs may have logged in recently.

Google Webmaster Tools was once Google Webmaster Wasteland. But the past year has been a fruitful one as Webmaster Tools has rolled out improvements faster than Facebook does new privacy statements. Google Webmaster Tools (GWT) is now full of insightful data and metrics that you cannot get anywhere else. Some GWT data is useful, some is not. Let's dive in and take a look at each tool in GWT.
Guide to Google Webmaster Tools Index Webmaster Tools Sections My Favorite Tools
Configuration #1. Download Your Latest Links
Health #2. View Your Website Crawl Stats
Traffic #3. Submit To Index
Optimization #4. Webmaster Tools Data in Google Analytics
Labs #5. Rich Snippets/Structured Data Test Tool

Webmaster Tools Home

When you first login, you'll see a list of all websites in your Google Webmaster tools account as well as few links to view all messages from Google, 'Preferences', 'Author Stats' (Labs), and a few miscellaneous links under 'Other Resources'.


All Messages

Google used to rarely communicate with Webmasters through messages. This year some probably wish they communicated a little less with the amount of "love notes" many SEOs have received. You might see a message here if:
Google thinks your site may have been hacked
Google detected unnatural links pointing to your site
Google thinks links pointing to your site are using techniques outside Google’s Webmaster Guidelines

You can set the messages email threshold to: 'only important' or 'all messages' under the "Preferences" tab

See it: View All Your Messages
Labs - Author Stats



Since authorship isn't tied to a single domain, Google shows authorship stats for all sites you write for as well as individual stats. You'll need a valid author profile (go Google+!) to see stats here. The stats are interesting, and good for verifying which URLs are showing your ugly mug in the SERPs.

See it: View your Author Stats

Other Resources - Rich Snippets/Structured Data

If you've never used the rich snippets testing tool, now known as "structured data", bookmark it now. It's a one stop shop to test URLs to see if your author profile is linked correctly.

You can also use the tool to check if you've setup or verified your:
Author Page
Name
Google+ Page as a Publisher
Any structured data detected (reviews, products, song titles, etc) in the form of microdata, microformats, or RDFa

See it: Test Your URLs for Structured Data
Specific Site Dashboard in Google Webmaster Tools

Once you select a site after logging in, you see the real meat of the tool. The site specific dashboard has a nice overview showing:
Crawl Errors
URL Errors
Site Errors
Health status of DNS, Server Connectivity & Robots.txt
Overview of # of Queries (plus clicks and impressions)
Sitemaps (including submitted URLs and indexed URLs)



There are five major sections once you've selected a site: 'Configuration', 'Health', 'Traffic', 'Optimization', and 'Labs'. I find that the most insightful data is in the 'Heath' and 'Traffic' sections, and what you can get inside Google Analytics.

The 'Configuration' Section
Settings



Here you can target a specific country for your website, choose a preferred domain (www or non-www), and limit the crawl rate of Googlebot if you so choose.
Sitelinks



Google automatically choosing Sitelinks to display below your main URL on certain queries, usually brand related. If you have certain URLs you wouldn't want showing as Sitelinks you can "demote" them and Google won't show those demoted URLs.
URL Parameters

If you're having problems with duplicate content on your site because of variables/parameters in your URLs you can restrict Google from crawling them with this tool. Unless you're sure about what you're restricting, don't play with the settings here!
Change of Address

If you are switching your site to a whole new domain, do a 301 redirect, then make sure Google knows about it here.
Users

Ever taken like 20 minutes to add a new user to your Google Analytics account? No? OK, maybe that was just me. Luckily adding a user to GWT is much easier. There are two main user types: 'Full user' and 'Restricted User'. Restricted users are good for clients if you want to give them most view-only access, but little ability to change settings or submit things (you probably don't clients filing random reconsideration requests!).


Associates

This setting is a way for members of YouTube's Partner Program (probably not you) to link their YouTube Channel with Webmaster Tools. My guess is this section will get more settings in the future, but for now, it's very confusing. More details on the Google Webmaster Central blog here.

The 'Health' Section
Crawl Errors

Crawl errors shows you issues Googlebot had in crawling your site. This includes response codes (404s, 301s) as well as a graph of the errors over time. This is a fantastic resource for spotting broken links, as the URL shows up as a 404 error. You can see when Google first detected the error codes and download the table of errors into a spreadsheet.



Crawl Stats

Pages crawled per day is a good SEO metric to track over time. You can get some insight from the chart, but this is a metric to check in on and record every week. Ideally you want that number continuing to climb, especially if you are adding new content.



Blocked URLs Fetch as Googlebot & Submit To Index

Fetch as Googlebot will return exactly what Google's spider "sees" on the URL you submit. This is handy for spotting hacked sites as well as seeing your site the way Google does. It's a good place to start an SEO audit.

The really neat feature that's new this year is "Submit to Index". Ever made a title tag change and wished Google would update its index faster to get those changes live? 'Submit to Index' does just that. 50 times a month you can submit a page to update in near real-time in Google's index. Very handy for testing on-page changes.

Here's Matt Cutts on how to use the 'Submit to Index' tool:


Index Status

Make sure and hit the 'Advanced' button here so you can see all the interesting index stats Google shows about your site. Keep an eye on the 'Not Selected' number as that could indicate that Google is not viewing your content favorably or you have a duplicate content issue if that number is rising.


Malware

If Google has detected any malware on your site you will see more information here. Google often sends messages now if Malware is detected as well.

The 'Traffic' Section
Search Queries

These queries are when your site shows up in a search result, not just when someone clicks your site. So you may find some keyword opportunities where you are showing up but not getting clicks. I much prefer the interface in Google Analytics for this query data, and you may find a lot more queries showing up there then here.

Keep an eye on the CTR % for queries. If you have a known #1 ranking (your brand terms for example) for but an abnormally low position 1 CTR that's a sign that someone might be bidding on your brand terms (which may or may not be good). If you have a high position but low CTR it usually indicates that your meta descriptions and title tags may not be enticing enough. Can you add a verified author to the page? Or other structured data? That could help CTR rates.



Links To Your Site

This is my favorite addition to GWT this year. The link data here keeps getting updated faster and faster. When this was first launched earlier this year the delay on finding links was around three weeks. I've seen the delay down to as little as one week now.

There are two ways to download lists of links, but the "Download Latest Links" is the more useful of the two.

"Download More Sample Links" just gives a list of the same links as the latest links but in alphabetical order instead of most recent. The main report lists the domains linking to your site sorted by the number of links. Unfortunately drilling down into the domain level doesn't give really any useful insights other than the pages that are linked too (but you can't see where they are linked from on the domain). You'll find domains listed here but not in the "Latest Links" report. Bummer.


Internal Links

Pretty good report for diagnosing internal link issues. This tool is nothing fancy but URLs are sorted by most internal links. Use this to diagnose pages on your site that should be getting more internal link juice.

The 'Optimization' Section
Sitemaps

See a list of all the different types of sitemaps Google has found or that you have added and some stats about each one. You can also test a sitemap as well before submitting it and Google will scan to find any errors. Webmaster Tools shows stats here on Web sitemaps, as well as Video, News, and Image sitemaps as well
Remove URLs

You can submit URLs (only for sites you control of course) that you wish removed from Google. Make sure and follow the removal requirements process.
HTML Improvement

Think of this as a basic On-Page SEO audit tool. Google will show you lists of URLs on your site that don't have unique Title Tags, or are missing Meta Descriptions. This is a handy tool for quick On-Page SEO issues when you first take over a new website. Click on any of the issues found to return a list of the URLs that need improvement.


Content Keywords

See a list of single keywords, not key phrases, which Google thinks your site is about. As long as you don't see spam stuff here, you're good.
Structured Data

If you have some structured data on your site, such as a linked Google+ author or product review data, you can see stats about that data including the type of data found and the schema. This is useful to mass verify that all the pages you think are marked up correctly actually are.



The 'Labs' Section
Custom Search

Ever wanted to build your own search engine? You can with Google Custom Search. If you have a collection of sites that you're always searching through using Google, you might consider using Google Custom search to build your own Google that just returns results from those sites. You can see how the custom search engine would work on just your own site using the preview tool here in Webmaster Tools.
Instant Previews

Input any URL on your site (or just leave blank and click 'Compare' to see the homepage) to see what the preview of the site might look like in a Google desktop search results set, or on a mobile SERP.


Site Performance

This tool got dropped by Google's spring cleaning in April 2012. I like using webpagetest.org for testing site performance.

Webmaster Tools Data In Google Analytics

Connecting your Google Analytics account with your verified site profile in Google Webmaster tools brings some GWT data directly into your Google Analytics account. No need to login to two places.

To connect a verified GWT site to the correct analytics site, click the "manage site" dropdown:



Once connected, GWT data shows up in the Standard Reporting section of Google Analytics under "Traffic Sources" -> "Search Engine Optimization".

Not all GWT data is available in GA. You'll only get three data sets in Google Analytics:
Queries
Landing Pages
Geographical Summary

Let's look at each of these and see what's worth looking at.
Queries

Queries are interesting because you can see some of the keywords that might be hidden under (not provided). This doesn't help with attribution of course, but at least we can still use that data for keyword research. Darn you (not provided).

What's really interesting is how many more queries show up in the query report in Google Analytics (that is supposed to be GWT data) than do when you directly get the query data in Google Webmaster Tools. For example, for the timeframe: Oct 28th-Nov 27th we had 317 queries report in Google Analytics:



but only 93 in the Google Webmaster Tools 'Top queries' report:



I'm not sure why such a big discrepancy between GWT queries and queries in Analytics from GWT. I definitely see more Google Images type queries in the GA report and less in the 'Top Queries' in GWT. Interesting discrepancy. Anyone else notice a big difference in query data?

Nonetheless the Query data can be interesting and it's nice to have right in GA. I hope that Google continues to provide more GWT data directly into Google Analytics like this.
Landing Pages

You're better off getting your actual top landing pages list from Analytics, but you can see what GWT sees as your tops pages sorted by Impressions. The interesting nugget of info here is the CTR. That's not data you see in analytics and could be insightful. I like comparing the CTR to the site average:


Geographical Summary

This section is again useful really for the CTR rate data. Looking at specific countries you can see where it might be worth running more Facebook ads or doing some international SEO work in.

Source:seomoz.org