My work ranges from design research to wireframing and coding.
I don't have all of my details from my work, so this is an overview of the methods I use:
Information architecture: I've used a range of tools from Optimal Sort to good old fashioned cards on a table. I'm also a big fan of Excel Content Inventories — as boring as they may look, they're a quick and easy way to get an overview of an existing site structure. And they're easy to share and edit, even with clients.
Wireframing: I'll set this out in Indesign (partly as I'm often sending documentation digitally, also it's easier to use in a design studio as most have it installed even if they don't have Omnigraffle or Visio). I've been using a customised version of the Eight Shapes Unify templating system as a wireframing and documentation tool for a few years (sometimes I hand annotate documents with a Wacom). I'll usually integrate this with design work in Illustrator or Photoshop (depending on how photoheavy the design is).
Coding (front-end and PHP): I admit to using Dreamweaver in the old days (always handcoding, mind!) but these days use TextWrangler as it's fast and lightweight. (As a Mac user, I'm interested in Coda but haven't needed a reason to work with it as of yet). I have done some work with HTML5. CMS development: I'll happily work with Wordpress and Drupal (working locally with MAMP). I've used Mercurial for collaborative work.