I have some Firefox addons to manage my daily seo stuff like "Quirk search status" which shows alexa, PR, backlinks and other important stuff it also comes with an option to highlight nodofollow links and that really helps me when i comment on blogs. in short its a good time saver.
mostly i use search status as i am link builder so i can completely analyze other sites from i am taking link with search status other then it i use wordtracker for keyword research
SeoMoz Tools Majestic SEO Web Developer Toolbar Plugin for Firefox (very useful!) Rex Swain HTTP Viewer (useful for complicated redirects) Google Webmaster Tools Google Analytics I think theres a few more but can't think at the minute! HTH
I use SEOmoz and Traffic Travis for my projects and rankings. I use Piwik for analytics. I use Wordpress for my sites but I'm looking into Joomla for those now.
I'm using "PHP meets SEO - Google Ranking Check " to check my rankings is free and you can run it via crons on your server.
In seo lots of tools available on net you can chose them by your usability. I use yahoo site explorer to check backlink, google keyword tool to analysis keyword , google tool bar for check site pr , alexa.com to check alexa rank of site. add ons are also helpful in seo.