Advanced Link Manager  - Performs deep crawl analysis of links for any site by crawling all linking sites and providing analysis of links by domain and gains/losses over time as well as PageRank. Also, fully manages extensive reciprocal linking through one tool.

Advanced Web Ranking - Keeps track of all your rankings and competitor sites at the page level, and maintains historical results for performance analysis. Also, generates numerous reports at the keyword or URL level, and compares the results over time and against competing sites.

Agent Web Ranking - Rankings checker; simulates a browser approach.

Archive.org  - Historical Web page archive. 

ClickTracks - Search analytics and PPC management.

Combine Words - Free keyword list expansion tool.

Deep Link Ratio checker - Analyzes how the deep link ratio of a site affects its rank in search engines. DLR is the proportion of inbound links into all pages of your Web site, compared to inbound links pointed at the homepage. 

Domain Age checker tool  - It is widely accepted by most SEOs that domain age factors into the trustworthiness of a site. The longer the domain has had a positive history with the engines, the better.

Domain Stats - Quick hit site stats.

Elixir Link Quality Tool - Another nice tool that gives a quick overview of search elements for a given domain.

Firefox add-ons - Too many to list here, they include Live HTTP headers and Searchstatus. 

Google Adwords Editor - Allow you to download your AdWords account to your computer, make your changes, and then upload your revised campaigns. Work off line, copy and paste, do bulk changes, then upload all at once.

Google Adwords Keyword Tool - Provides new keyword ideas.

Google Cheat Sheet - Two-page quick reference guide to Google search products and useful operators.

Google Suggests - As you type into the search box, Google guesses what you're typing and offers suggestions in real time.

Google Toolbar - Checks PageRank, provides shortcuts to various Google properties -- though some SEMs choose not to use it, citing the amount of personal data it captures.

Google Traffic Estimator - Tool provides quick traffic estimates of keywords

Google Trends - Shows trends in search popularity.

Google Webmaster Central  -  One-stop shop for Webmaster resources.

Google Website Optimizer - Google's free multivariate and A/B testing tool, helps online marketers increase visitor conversion rates and overall visitor satisfaction by continually testing different combinations of site content (text and images).

Hitwise - Provides competitive insights on keywords.

ISAPI Rewrite  - Rewrites URLs at the server level for IIS (similar to mod rewrite for Apache).

KW Density/Frequency Analyzer - Most keyword "density" tools don't really show density or weighted terms - they show frequency.  Still, they can be handy for educating copywriters, or analyzing longer documents.

Marketleap Search Engine Saturation tool - Comprehensive backlink and page saturation tool.  One of the first free tools of its kind that was publicly available to anyone who wanted to use it.

MSN adCenter Tools - Toolbox of advertising and keyword research tools including clickstream analysis and more.

Non-Personalized Google Search Plugin -  If you are logged in to any Google service - Adwords, Gmail, etc., then Google takes the liberty of showing you personalized results, which are different from the "objective" results that the rest of the world sees.  This tool allows you to remain logged in to Google Services while viewing nonpersonalized search results.

Overture's Keyword Selector Tool -  Provides  popularity numbers from Yahoo.  Good for keyword brainstorming.  It's a little bit like search engine Groundhog Day, because all of the results are stuck in January 2007.

Quintura - Visual search navigation tool that extracts keywords from Yahoo! search results, and builds a word cloud.  Good for keyword brainstorming.

Search Engine Relationship Chart - Visual diagram of search engine distribution relationships.

SEO Toolbar for Firefox - Gets back link info by domain type, domain age, PageRank, Alexa rank, cache date and more, right on the search results page -- along with many other features, too numerous to list here. 

SEODigger.com - Competitive ranking report tool, shows ranking history in Google. 

Server Header Checker - Allows you to check the HTTP status returned by a server.  Useful for checking redirect status (301, 302, etc.).  One example of many other tools that perform a similar function.

Site Explorer - Yahoo!'s back link and indexed page count tool.

TouchGraph.com - Free link node mapping and visualization tool, good for educating clients on how link networks work.

Trellian/KeywordDiscovery.com - Provides keyword ideas and aids in brainstorming.  The group agreed that most SEMs have chosen this tool as a standard for directional keyword search frequency.

VeriClix - A free pay-per-click auditing and click fraud monitoring tool. (Disclosure:  DFWSEM board member Jeff Martin operates VeriClix).

WatchFire WebXact  - Site diagnostics tool.  Assesses broken links, checks meta tags, code validation, etc.

We Build Pages' Toolset - Free SEO Toolset, including back link and anchor text checker, class C back link analyzer, keyword density (frequency) analysis tool, spider viewer and many more.

Web Position Gold - Checks natural search engines rankings.

WordTracker - Provides new keyword ideas; helpful for brainstorming and discovering new keyword ideas.