The Layout itself is a pretty good and an effective layout. I could easily tell that this isn't your first attempt at it (especially since you are providing web-master tools

), but that's beside the point. I think you got a pretty effective layout there.
I like the fact that you have a lot of images and different colors in there. It is a real good plus for people who are more visual at things than others. Like me

I like how you got your footer and header set up there... really looks professional (at least I think so). The description of tools are too the point and explain everything well. I know what each tool does without even trying them out. All this is coming from the first page so far... I haven't really explored the site yet.
You could use the © to create the copyright symbol rather than typing (c) in the footer... although doing that could add a little more bits to the loading of the page, but I don't think that that would make much of a difference or a loading lag.
The site loads pages pretty quickly. That is really good especially for people like me... people who barely have any patience on the web. I usually wait for 5 seconds, and if the page is not loaded I would leave... unless I really need the information.
I believe that the link titled "SEO Articles" is what I consider to be a misnomer. It should be called "Web Articles" or something of that effect. SEO is search engine optimization (I know you know... I'm saying that to keep my thoughts intact) so the link title implies that the articles are about SEO... a specialized topic.
What you got though is a mix of SEO and other web/font related articles. Maybe just title it "Articles"? Short and to the point, like all those descriptions of tools you got there on the first page.
I think that there is too much space above the comments. There is literally like 5 inches of whitespace from the article and the comments... I just think that is a waste of calories (I got to scroll more

).
Your code could do some cleaning up. I don't know how much of importance you put on valid coding, but I put a lot of value to that. I think that you should fix all the validation errors on all of your pages.
You also have like 5 inches of whitespace between the article title and the horizontal line above it. You should shorten that distance. (Once again, a waste of calories and space...).
I don't know if you made the design but I think you should make both versions of your design (Narrow and Wide) fluid... otherwise make the
Wide version the default version since it's more fluid. It just forgives the shorter resolutions and people who can't afford bigger resolutions in this economy.
I don't know how long you had the site, how many people used/uses your site, and of your site's on-line reputation, but I think that gears are beginning to be overused to represent webmaster tools workshop or w/e. Not telling you that the logo sucks or anything because it doesn't... I'm just saying.
I can't bring any examples to mind right now, but every time I see a gear or gears as a logo there is a fleeting moment of de-ja-vu.
The title for the search is "Custom Search"... maybe change that to something more original or something that doesn't seem like it came from a page generator? Something like, "Search Webtoolhub", or just, "Search" or something to that effect? Not that I'm picky, the current title works, but when I saw that, I thought it was Google that was doing it. (It might though... )
Also, why does sitemap open in a new window? Or the Webmaster tools? I see that you done that intentionally (based on the images besides those links), but why? Maybe I'm missing out on something or just didn't learn something, but I don't see anything in that.
Why should I register? I see a link to log-in and a link for new users to register... but nowhere does it tell me what additional features I would get after registering. Maybe I missed something, but I can't find it. The log-in says that "Joining is as simple as 1,2,3...", but it doesn't tell me why.
The FAQs are also staying silent about it, and so does the rest of the site it seems. I couldn't find it anywhere. Maybe you could right a little bit and tell me "Why" to register after the "Joining is as simple as 1,2,3..." and on the actual register page... maybe in the FAQs as well... the question would be, "Why should I register?".
Maybe you did tell me why and I completely overlooked it... or there is a service that requires user-recognition and I overlooked that service, but I can't find such service there... I know that "My Tools" has to do something with it, but I fail to see how user-recognition is required there.
There are other pages like the Banner page that has extra space at the bottom or other places. I suggest fix those...
I applaud you on your successful placement of links and user-friendliness (outside of the membership service... ) I'm only talking about the site outside of the membership place... haven't registered or logged in... but so far so good.
The site is easy to navigate through and the links are in logical order (or so as I see it), so I don't have anything against that.
I think I'm done with this novel right now... I just might have depleted my ideas on your site

Good job, I think that you have done a good job overall.