The following is a quick reference guide to the Drupal modules that I use on every site with specific requirements, settings and tips.

Clean URLs (core) - Administer > Site Configuration > Clean URLs
Run Clean URL test. If you don't pass, add 'RewriteBase /' to .htaccess file; add '$conf['clean_url']=1;' to site/default/settings.php.
Apache server only.

Pathauto - Administer > Site Configuration > Pathauto
5.x-2.0 - requires Path (core), Token
Node settings - [termalias]/[title-raw].htm
Category Settings - [catpath-raw]
5.x - 1.0 - Requires Path (core)
Node settings - [catalias]/[title].htm
Category settings - [catpath]
Download Pathauto

Global Redirect - requires no configuration
Download Global Redirect

Page Title - Administer > Content Management > Page Titles
5.x 2.0 - Requires Token
Add function _phptemplate_variables to template.php file, specified in the readme.txt file.
Download Page Title

Nodewords (Meta Tags) - Administer > Content Management > Meta Tags
Check only Keywords and Descriptions for edit forms and html output
Download Nodewords/Meta Tags

Taxonomy (core) - Administer > Content Management > Categories
Add Vocabulary. Enable content type (Book), Single hierarchy, Required
Add Terms - List your site categories here (Silos)

Book (core) - Create Content > Book Page
Turn on Book Navigation block at Administer > Site Building > Blocks
Select Parent and Category terms

XML Sitemap - Adminster > Site Configuration > XML Sitemap
Under search engines, enable log access
Add personal webmaster data
Download XML Sitemap

Module Weight - Requires no configuration
Set the weight for XML Sitemap to 10
Download Module Weight

.htaccess file
Uncomment the rewrite conditions to redirect all users to access the site WITH the 'www' prefix

robots.txt
Download the improved robots.txt file that fixes some problems and adds additional files to the list